Login

u/fondow

r/PikaOS r/DrWillPowers
▲ 8 r/DrWillPowers

My BAM gene.iobio.io list

For the VCF variants and a small AI summary, see https://www.reddit.com/r/DrWillPowers/s/ALocEnyebC

BAM variants

  1. ABCB1 — Missense variant

- Gene: ABCB1

- Variant: SNP 7:87549888 T→A

- Protein: p.Glu506Val

- HGVSc: ENST00000622132.5:c.1517A>T

- rsID: —

- Zygosity: Het

- Ref Allele: T

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.671

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 5.04)

- Reads: 51

---

  1. ABCB8 — Missense variant

- Gene: ABCB8

- Variant: SNP 7:151028586 G→A

- Protein: p.Arg24His

- HGVSc: ENST00000358849.9:c.71G>A

- rsID: rs761485323

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00000657 AF · 0.0000241 max ancestry · 1 alt / 152 240 total · 0 hom

- REVEL: 0.302

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−0.323)

- Reads: 42

---

  1. ABCC5 — Missense in non-canonical transcripts

- Gene: ABCC5

- Variant: SNP 3:183987742 A→T

- Protein: — (intronic on MANE; missense in ENST00000427120)

- HGVSc: ENST00000334444.11:c.591+28T>A

- rsID: rs140530675

- Zygosity: Het

- Ref Allele: A

- Alt Allele: T

- gnomAD genomes v4: 0.000341 AF · 0.000588 max ancestry · 52 alt / 152 274 total · 1 hom

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.401)

- Reads: 43

---

  1. ACE — Missense variant

- Gene: ACE

- Variant: SNP 17:63497235 T→A

- Protein: p.Phe1264Ile

- HGVSc: ENST00000290866.10:c.3790T>A

- rsID: —

- Zygosity: Het

- Ref Allele: T

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.055

- Quality: Poor evidence of alternate allele

- Conservation: Marginally conserved (0.77)

- Reads: 46

---

  1. AKR1B10 — Frameshift variant

- Gene: AKR1B10

- Variant: INS 7:134537643 C→CA

- Protein: p.Thr244AsnfsTer29

- HGVSc: ENST00000359579.5:c.730dup

- rsID: rs1333065534

- Zygosity: Het

- Ref Allele: C

- Alt Allele: CA

- gnomAD genomes v4: 0.00 AF · 0 alt / 0 total · 0 hom

- gnomAD exomes: 0.00000616 AF

- REVEL: —

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 4.759)

- Reads: 33

---

  1. APOB — Missense variant (Hom)

- Gene: APOB

- Variant: COMPLEX 2:21009931 TG→CA

- Protein: p.Ile2313Val

- HGVSc: ENST00000233242.5:c.6936_6937Inv

- rsID: rs386643884

- Zygosity: Hom (37 alt, 0 ref)

- Ref Allele: TG

- Alt Allele: CA

- gnomAD genomes v4: 0.00 AF

- ClinVar: Benign/likely benign — Familial hypobetalipoproteinemia 1, Hypercholesterolemia autosomal dominant type B

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−0.386)

- Reads: 37

---

  1. APOB — Frameshift variant

- Gene: APOB

- Variant: DEL 2:21007941 TA→T

- Protein: p.Tyr2976MetfsTer27

- HGVSc: ENST00000233242.5:c.8926del

- rsID: —

- Zygosity: Het

- Ref Allele: TA

- Alt Allele: T

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 5.416)

- Reads: 35

---

  1. ARID1B — Missense variant (Gly587Asp)

- Gene: ARID1B

- Variant: SNP 6:156779440 G→A

- Protein: p.Gly587Asp

- HGVSc: ENST00000636930.2:c.1760G>A

- rsID: rs1226692763

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- ClinVar: Uncertain significance

- REVEL: 0.171

- Quality: Poor evidence of alternate allele

- Conservation: Marginally conserved (0.224)

- Reads: 23

---

  1. ARID1B — Missense variant (Ala50Ser)

- Gene: ARID1B

- Variant: SNP 6:156777828 G→T

- Protein: p.Ala50Ser

- HGVSc: ENST00000636930.2:c.148G>T

- rsID: —

- Zygosity: Het

- Ref Allele: G

- Alt Allele: T

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Questionable sequence depth

- Conservation: Not conserved (−0.228)

- Reads: 8

---

  1. ARID1B — Missense variant (Pro1299Thr)

- Gene: ARID1B

- Variant: SNP 6:157184411 C→A

- Protein: p.Pro1299Thr

- HGVSc: ENST00000636930.2:c.3895C>A

- rsID: —

- Zygosity: Het

- Ref Allele: C

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.124

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 4.948)

- Reads: 37

---

  1. ARID2 — Missense variant

- Gene: ARID2

- Variant: SNP 12:45905056 A→G

- Protein: p.Lys1829Arg

- HGVSc: ENST00000334344.11:c.5486A>G

- rsID: —

- Zygosity: Het

- Ref Allele: A

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.023

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 2.542)

- Reads: 38

---

  1. ATP5F1B — Missense variant

- Gene: ATP5F1B

- Variant: COMPLEX 12:56642557 GATT→CATA

- Protein: p.Ile325Met

- HGVSc: ENST00000262030.8:c.972_975delInsTATG

- rsID: —

- Zygosity: Het

- Ref Allele: GATT

- Alt Allele: CATA

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 9.129)

- Reads: 70

---

  1. AVPR1A — Missense variant

- Gene: AVPR1A

- Variant: SNP 12:63147394 A→G

- Protein: p.Ser408Pro

- HGVSc: ENST00000299178.4:c.1222T>C

- rsID: —

- Zygosity: Het

- Ref Allele: A

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.180

- Quality: Poor evidence of alternate allele

- Conservation: Not conserved (−0.463)

- Reads: 42

---

  1. BRD4 — Missense variant

- Gene: BRD4

- Variant: SNP 19:15243196 A→G

- Protein: p.Leu958Pro

- HGVSc: ENST00000679869.1:c.2873T>C

- rsID: rs955003930

- Zygosity: Het

- Ref Allele: A

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.151

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.693)

- Reads: 22

---

  1. CAT — Missense variant

- Gene: CAT

- Variant: SNP 11:34456041 G→A

- Protein: p.Glu248Lys

- HGVSc: ENST00000241052.5:c.742G>A

- rsID: —

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.457

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 4.226)

- Reads: 38

---

  1. CHD3 — Inframe deletion in non-canonical transcripts

- Gene: CHD3

- Variant: DEL 17:7884893 CGAG→C

- Protein: — (upstream gene variant on MANE; inframe deletion in ENST00000380358 / ENST00000700753)

- HGVSc: —

- rsID: rs770383628

- Zygosity: Het

- Ref Allele: CGAG

- Alt Allele: C

- gnomAD genomes v4: 0.000322 AF · 0.000845 max ancestry · 45 alt / 139 660 total · 0 hom

- ClinVar: Benign

- REVEL: —

- Quality: Questionable sequence depth

- Conservation: Highly conserved (phyloP 2.282)

- Reads: 7

---

  1. CHD3 — Frameshift variant

- Gene: CHD3

- Variant: DEL 17:7910504 AC→A

- Protein: p.Ile1892SerfsTer49

- HGVSc: ENST00000330494.12:c.5673del

- rsID: —

- Zygosity: Het

- Ref Allele: AC

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 5.742)

- Reads: 23

---

  1. COMT — Missense variant (Gly15Leu)

- Gene: COMT

- Variant: COMPLEX 22:19962569 GG→CT

- Protein: p.Gly15Leu

- HGVSc: ENST00000361682.11:c.43_44delInsCT

- rsID: —

- Zygosity: Het · multiallelic

- Ref Allele: GG

- Alt Allele: CT

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.878)

- Reads: 29

---

  1. COMT — Missense variant (Leu18Gln)

- Gene: COMT

- Variant: SNP 22:19962579 T→A

- Protein: p.Leu18Gln

- HGVSc: ENST00000361682.11:c.53T>A

- rsID: rs1439513393

- Zygosity: Het

- Ref Allele: T

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- gnomAD exomes: 0.00000213

- REVEL: 0.397

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−0.518)

- Reads: 79

---

  1. CYP2C19 — Missense variant

- Gene: CYP2C19

- Variant: COMPLEX 10:94842865 CA→TG

- Protein: p.Ile331Val

- HGVSc: ENST00000371321.9:c.990_991Inv

- rsID: rs1554854489

- Zygosity: Het · multiallelic

- Ref Allele: CA

- Alt Allele: TG

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−1.101)

- Reads: 16

---

  1. CYP2D6 — Missense variant

- Gene: CYP2D6

- Variant: SNP 22:42127481 C→T

- Protein: p.Arg380His

- HGVSc: ENST00000645361.2:c.1139G>A

- rsID: rs61731586

- Zygosity: Het

- Ref Allele: C

- Alt Allele: T

- gnomAD genomes v4: 0.00217 AF · 0.00376 max ancestry · 310 alt / 142 762 total · 0 hom

- REVEL: 0.140

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.243)

- Reads: 27

- Note: Low coverage exons (1)

---

  1. CYP21A2 — Missense variant

- Gene: CYP21A2

- Variant: SNP 6:32041127 G→A

- Protein: p.Ser494Asn

- HGVSc: ENST00000644719.2:c.1481G>A

- rsID: rs6473

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00566 AF · 0.0182 max ancestry · 782 alt / 138 240 total · 0 hom

- ClinVar: Benign — Classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency

- REVEL: 0.076

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.828)

- Reads: 40

---

  1. DRD4 — Missense variant

- Gene: DRD4

- Variant: SNP 11:640099 A→C

- Protein: p.Ser284Arg

- HGVSc: ENST00000176183.6:c.850A>C

- rsID: rs34662058

- Zygosity: Het

- Ref Allele: A

- Alt Allele: C

- gnomAD genomes v4: 0.000572 AF · 0.00439 max ancestry · 55 alt / 96 084 total · 2 hom

- REVEL: 0.043

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−1.067)

- Reads: 13

- Note: Low coverage exons (1)

---

  1. EHMT1 — Splice acceptor in non-canonical transcripts

- Gene: EHMT1

- Variant: SNP 9:137743390 A→T

- Protein: p.Leu281Phe (ENSP00000417980.1)

- HGVSc: ENST00000460843.6:c.843A>T

- rsID: rs1485591700

- Zygosity: Het

- Ref Allele: A

- Alt Allele: T

- gnomAD genomes v4: 0.0000156 AF · 0.0000329 max ancestry · 2 alt / 128 284 total · 0 hom

- Most severe impact: Splice acceptor in ENST00000478940

- REVEL: 0.074

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 6.733)

- Reads: 26

---

  1. EHMT2 — Missense variant

- Gene: EHMT2

- Variant: SNP 6:31884660 T→C

- Protein: p.Tyr863Cys

- HGVSc: ENST00000375537.9:c.2588A>G

- rsID: —

- Zygosity: Het

- Ref Allele: T

- Alt Allele: C

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.370

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 2.75)

- Reads: 36

---

  1. EP400 — Inframe deletion

- Gene: EP400

- Variant: DEL 12:131961900 AGAG→A

- Protein: p.Glu437del

- HGVSc: ENST00000389561.7:c.1296_1298del

- rsID: rs752787745

- Zygosity: Het

- Ref Allele: AGAG

- Alt Allele: A

- gnomAD genomes v4: 0.000335 AF · 0.000412 max ancestry · 51 alt / 152 314 total · 0 hom

- REVEL: —

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 3.72)

- Reads: 36

---

  1. EP400 — Inframe insertion

- Gene: EP400

- Variant: COMPLEX 12:132062545 ACAA→GCAACAGCAG

- Protein: p.Gln2747_Gln2748dup

- HGVSc: ENST00000389561.7:c.8178_8181delInsGCAACACGCAG

- rsID: —

- Zygosity: Het · multiallelic

- Ref Allele: ACAA

- Alt Allele: GCAACAGCAG

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 4.261)

- Reads: 11

---

  1. FOXO3 — Inframe deletion

- Gene: FOXO3

- Variant: DEL 6:108561444 TCGG→T

- Protein: p.Gly84del

- HGVSc: ENST00000406360.2:c.249_251del

- rsID: rs372569038

- Zygosity: Het

- Ref Allele: TCGG

- Alt Allele: T

- gnomAD genomes v4: 0.00000678 AF · 0.0000151 max ancestry · 1 alt / 147 426 total · 0 hom

- REVEL: —

- Quality: Poor evidence of alternate allele

- Conservation: Not conserved (−0.543)

- Reads: 24

---

  1. GABRA3 — Missense variant, splice region variant

- Gene: GABRA3

- Variant: SNP X:152345700 A→G

- Protein: p.Leu48Pro

- HGVSc: ENST00000370314.9:c.143T>C

- rsID: —

- Zygosity: Het (hémizygote — chrX, sujet XY)

- Ref Allele: A

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.423

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 3.43)

- Reads: 23

---

  1. HDAC9 — Missense variant

- Gene: HDAC9

- Variant: SNP 7:18954219 T→C

- Protein: p.Ile1004Thr

- HGVSc: ENST00000886413.1:c.3011T>C

- rsID: rs138163349

- Zygosity: Het

- Ref Allele: T

- Alt Allele: C

- gnomAD genomes v4: 0.00209 AF · 0.00334 max ancestry · 318 alt / 152 234 total · 4 hom

- ClinVar: Benign

- REVEL: 0.051

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.848)

---

  1. HTR1D — Missense variant

- Gene: HTR1D

- Variant: SNP 1:23193766 C→A

- Protein: p.Ala152Ser

- HGVSc: ENST00000374619.2:c.454G>T

- rsID: rs142643700

- Zygosity: Het

- Ref Allele: C

- Alt Allele: A

- gnomAD genomes v4: 0.000440 AF · 0.000544 max ancestry · 67 alt / 152 202 total · 0 hom

- ClinVar: Uncertain significance

- REVEL: 0.121

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−3.894)

- Reads: 38

---

  1. HTR6 — Missense variant

- Gene: HTR6

- Variant: SNP 1:19666276 C→A

- Protein: p.Pro175Thr

- HGVSc: ENST00000289753.2:c.523C>A

- rsID: —

- Zygosity: Het

- Ref Allele: C

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.060

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 1.609)

- Reads: 48

---

  1. KAT6B — Missense in non-canonical transcripts

- Gene: KAT6B

- Variant: SNP 10:74843533 G→A

- Protein: — (intronic on MANE; missense in ENST00000648539 / ENST00000650434)

- HGVSc: ENST00000287239.10:c.621+55G>A

- rsID: rs138782403

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.0104 AF · 0.0175 max ancestry · 1591 alt / 152 290 total · 8 hom

- ClinVar: Likely benign

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.469)

- Reads: 42

---

  1. KDM4B — Splice donor variant, coding sequence variant

- Gene: KDM4B

- Variant: COMPLEX 19:5131544 AGGT→GGGG

- Protein: —

- HGVSc: ENST00000159111.9:c.1784_1785+2delInsGGGG

- rsID: —

- Zygosity: Het

- Ref Allele: AGGT

- Alt Allele: GGGG

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 2.185)

- Reads: 11

---

  1. KDM4B — Missense variant

- Gene: KDM4B

- Variant: COMPLEX 19:5131533 CGGAGA→GGGGGG

- Protein: p.Glu593Gly

- HGVSc: ENST00000159111.9:c.1773_1778delInsGGGGGG

- rsID: —

- Zygosity: Het

- Ref Allele: CGGAGA

- Alt Allele: GGGGGG

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−0.061)

- Reads: 14

---

  1. KDM5C — Stop gained

- Gene: KDM5C

- Variant: SNP X:53193495 C→T

- Protein: p.Trp1420Ter

- HGVSc: ENST00000375401.8:c.4259G>A

- rsID: —

- Zygosity: Het (hémizygote — chrX, sujet XY)

- Ref Allele: C

- Alt Allele: T

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 4.091)

- Reads: 20

- Note: Low coverage exons (6)

---

  1. KDM5C — Missense variant (Ser1287Arg)

- Gene: KDM5C

- Variant: SNP X:53194318 T→G

- Protein: p.Ser1287Arg

- HGVSc: ENST00000375401.8:c.3859A>C

- rsID: —

- Zygosity: Het (hémizygote — chrX)

- Ref Allele: T

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.111

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.141)

- Reads: 18

---

  1. KDM5C — Missense variant (Phe642Leu)

- Gene: KDM5C

- Variant: SNP X:53201687 A→G

- Protein: p.Phe642Leu

- HGVSc: ENST00000375401.8:c.1924T>C

- rsID: —

- Zygosity: Het (hémizygote — chrX)

- Ref Allele: A

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.859

- Quality: Questionable sequence depth

- Conservation: Marginally conserved (0.242)

- Reads: 7

---

  1. KDM5D — Missense variant

- Gene: KDM5D

- Variant: SNP Y:19715853 C→A

- Protein: p.Cys728Phe

- HGVSc: ENST00000317961.9:c.2183G>T

- rsID: —

- Zygosity: Het (hémizygote — chrY)

- Ref Allele: C

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 5.755)

- Reads: 22

---

  1. KDM6A — Missense variant

- Gene: KDM6A

- Variant: SNP X:45089759 C→A

- Protein: p.Leu1241Ile

- HGVSc: ENST00000611820.5:c.3721C>A

- rsID: —

- Zygosity: Het (hémizygote — chrX)

- Ref Allele: C

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.540

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 7.562)

- Reads: 13

- Note: Low coverage exons (1)

---

  1. KDM6B — Missense variant

- Gene: KDM6B

- Variant: SNP 17:7853303 G→T

- Protein: p.Ala1611Ser

- HGVSc: ENST00000448097.7:c.4831G>T

- rsID: rs141627015

- Zygosity: Het

- Ref Allele: G

- Alt Allele: T

- gnomAD genomes v4: 0.0000591 AF · 0.000118 max ancestry · 9 alt / 152 324 total · 0 hom

- ClinVar: Likely benign — Inborn genetic diseases

- REVEL: 0.071

- Quality: Sufficient depth and allele counts

- Conservation: Moderately conserved (1.113)

- Reads: 40

---

  1. KDM6B — Inframe deletion

- Gene: KDM6B

- Variant: DEL 17:7848540 TCAC→T

- Protein: p.Thr762del

- HGVSc: ENST00000448097.7:c.2283_2285del

- rsID: rs59627144

- Zygosity: Het

- Ref Allele: TCAC

- Alt Allele: T

- gnomAD genomes v4: 0.000455 AF · 0.00194 max ancestry · 61 alt / 134 132 total · 0 hom

- ClinVar: Benign/likely benign — KDM6B-related disorder

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−0.035)

- Reads: 30

---

  1. KMT2D — Missense variant

- Gene: KMT2D

- Variant: SNP 12:49051444 G→A

- Protein: p.Pro747Ser

- HGVSc: ENST00000301067.12:c.2239C>T

- rsID: —

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- ClinVar: Uncertain significance — Kabuki syndrome 1

- REVEL: 0.034

- Quality: Poor evidence of alternate allele

- Conservation: Not conserved (−1.187)

- Reads: 45

---

  1. MED16 — Missense variant

- Gene: MED16

- Variant: SNP 19:877029 C→T

- Protein: p.Ser502Asn

- HGVSc: ENST00000325464.6:c.1505G>A

- rsID: rs1245708023

- Zygosity: Het

- Ref Allele: C

- Alt Allele: T

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.117

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 7.352)

- Reads: 23

- Note: Low coverage exons (1)

---

  1. MECP2 — Missense variant (Pro188Leu)

- Gene: MECP2

- Variant: SNP X:154031301 G→A

- Protein: p.Pro188Leu

- HGVSc: ENST00000453960.7:c.563C>T

- rsID: rs61749701

- Zygosity: Het (hémizygote — chrX)

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- ClinVar: Uncertain significance — Severe neonatal-onset encephalopathy with microcephaly, Rett syndrome

- REVEL: 0.430

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 3.613)

- Reads: 14

- Note: Low coverage exons (2)

---

  1. MECP2 — Missense variant (Glu18Gly)

- Gene: MECP2

- Variant: SNP X:154097613 T→C

- Protein: p.Glu18Gly

- HGVSc: ENST00000453960.7:c.53A>G

- rsID: —

- Zygosity: Het (hémizygote — chrX)

- Ref Allele: T

- Alt Allele: C

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.362

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 1.802)

- Reads: 10

---

  1. MED12 — Stop gained

- Gene: MED12

- Variant: SNP X:71140705 C→T

- Protein: p.Gln2039Ter

- HGVSc: ENST00000374080.8:c.6115C>T

- rsID: —

- Zygosity: Het (hémizygote — chrX)

- Ref Allele: C

- Alt Allele: T

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 4.708)

- Reads: 14

- Note: Low coverage exons (5)

---

  1. MED12 — Missense variant (Ser654Arg)

- Gene: MED12

- Variant: SNP X:71124374 A→C

- Protein: p.Ser654Arg

- HGVSc: ENST00000374080.8:c.1960A>C

- rsID: —

- Zygosity: Het (hémizygote — chrX)

- Ref Allele: A

- Alt Allele: C

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.098

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 6.178)

- Reads: 18

---

  1. MED12 — Missense variant (Ser1670Ala)

- Gene: MED12

- Variant: SNP X:71135236 T→G

- Protein: p.Ser1670Ala

- HGVSc: ENST00000374080.8:c.5008T>G

- rsID: —

- Zygosity: Het (hémizygote — chrX)

- Ref Allele: T

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.225

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 5.838)

- Reads: 26

---

  1. MED24 — Missense variant

- Gene: MED24

- Variant: SNP 17:40019633 C→A

- Protein: p.Val956Leu

- HGVSc: ENST00000394128.7:c.2866G>T

- rsID: rs776539281

- Zygosity: Het

- Ref Allele: C

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- gnomAD exomes: 6.93e-7

- REVEL: 0.200

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 3.299)

- Reads: 54

---

  1. MFN2 — Missense in non-canonical transcripts

- Gene: MFN2

- Variant: SNP 1:12014474 A→G

- Protein: — (downstream gene variant on MANE; missense in ENST00000675298)

- HGVSc: —

- rsID: rs143440477

- Zygosity: Het

- Ref Allele: A

- Alt Allele: G

- gnomAD genomes v4: 0.00280 AF · 0.00550 max ancestry · 401 alt / 143 404 total · 2 hom

- ClinVar: Likely benign

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−0.765)

- Reads: 49

---

  1. MYO7A — Missense variant

- Gene: MYO7A

- Variant: SNP 11:77181582 G→A

- Protein: p.Gly966Asp

- HGVSc: ENST00000409709.9:c.2897G>A

- rsID: —

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.625

- Quality: Poor evidence of alternate allele

- Conservation: Marginally conserved (0.307)

- Reads: 25

---

  1. NSD1 — Missense variant

- Gene: NSD1

- Variant: SNP 5:177212121 G→C

- Protein: p.Ser1241Thr

- HGVSc: ENST00000439151.7:c.3722G>C

- rsID: rs138641637

- Zygosity: Het

- Ref Allele: G

- Alt Allele: C

- gnomAD genomes v4: 0.000670 AF · 0.00308 max ancestry · 102 alt / 152 134 total · 0 hom

- ClinVar: Likely benign — Sotos syndrome, Weaver syndrome

- REVEL: 0.049

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−0.071)

- Reads: 40

---

  1. SETD1A — Inframe deletion

- Gene: SETD1A

- Variant: DEL 16:30971487 ATCC→A

- Protein: p.Ser1058del

- HGVSc: ENST00000262519.14:c.3141_3143del

- rsID: rs777098458

- Zygosity: Het

- Ref Allele: ATCC

- Alt Allele: A

- gnomAD genomes v4: 0.000284 AF · 0.000460 max ancestry · 43 alt / 151 592 total · 0 hom

- REVEL: —

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 2.241)

- Reads: 24

---

  1. SETD1B — Missense variant

- Gene: SETD1B

- Variant: SNP 12:121814436 A→C

- Protein: p.Ile741Leu

- HGVSc: ENST00000604567.6:c.2221A>C

- rsID: rs1592980803

- Zygosity: Het

- Ref Allele: A

- Alt Allele: C

- gnomAD genomes v4: 0.0000747 AF · 0.000581 max ancestry · 8 alt / 107 082 total · 0 hom

- REVEL: 0.319

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 7.907)

- Reads: 12

- Note: Low coverage exons (1)

---

  1. SETD2 — Stop gained

- Gene: SETD2

- Variant: SNP 3:47120411 G→A

- Protein: p.Gln1409Ter

- HGVSc: ENST00000409792.4:c.4225C>T

- rsID: —

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Poor evidence of alternate allele

- Conservation: Not conserved (−0.412)

- Reads: 21

---

  1. SLC22A13 — Missense variant

- Gene: SLC22A13

- Variant: SNP 3:38275953 C→T

- Protein: p.Thr365Met

- HGVSc: ENST00000311856.9:c.1094C>T

- rsID: rs765934579

- Zygosity: Het

- Ref Allele: C

- Alt Allele: T

- gnomAD genomes v4: 0.0000394 AF · 0.000576 max ancestry · 6 alt / 152 224 total · 0 hom

- REVEL: 0.376

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−5.666)

- Reads: 47

---

  1. SLCO3A1 — Missense variant (Arg307Ser)

- Gene: SLCO3A1

- Variant: SNP 15:92104454 A→C

- Protein: p.Arg307Ser

- HGVSc: ENST00000318445.11:c.921A>C

- rsID: rs72655652

- Zygosity: Het

- Ref Allele: A

- Alt Allele: C

- gnomAD genomes v4: 0.0115 AF · 0.0168 max ancestry · 1758 alt / 152 250 total · 19 hom

- REVEL: 0.086

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 6.031)

- Reads: 40

---

  1. SLCO3A1 — Missense variant (Ser123Ala)

- Gene: SLCO3A1

- Variant: SNP 15:91916179 T→G

- Protein: p.Ser123Ala

- HGVSc: ENST00000318445.11:c.367T>G

- rsID: —

- Zygosity: Het

- Ref Allele: T

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.310

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 5.852)

- Reads: 48

---

  1. SOD2 — Missense variant

- Gene: SOD2

- Variant: SNP 6:159692745 G→C

- Protein: p.Gln48Glu

- HGVSc: ENST00000538183.7:c.142C>G

- rsID: rs1305834681

- Zygosity: Het

- Ref Allele: G

- Alt Allele: C

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.083

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 7.494)

- Reads: 57

---

  1. SOX9 — Missense variant

- Gene: SOX9

- Variant: SNP 17:72123629 C→A

- Protein: p.Pro258Thr

- HGVSc: ENST00000245479.3:c.772C>A

- rsID: rs1295597096

- Zygosity: Het

- Ref Allele: C

- Alt Allele: A

- gnomAD genomes v4: 0.00 AF

- gnomAD exomes: 6.84e-7

- REVEL: 0.309

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 3.076)

- Reads: 37

---

  1. STAT3 — Missense in non-canonical transcripts

- Gene: STAT3

- Variant: SNP 17:42329523 C→T

- Protein: — (intronic on MANE; missense in ENST00000677421)

- HGVSc: ENST00000264657.10:c.1233+31G>A

- rsID: rs112644937

- Zygosity: Het

- Ref Allele: C

- Alt Allele: T

- gnomAD genomes v4: 0.00121 AF · 0.00307 max ancestry · 185 alt / 152 328 total · 0 hom

- ClinVar: Likely benign

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.629)

- Reads: 35

---

  1. SULT1A2 — Missense variant

- Gene: SULT1A2

- Variant: COMPLEX 16:28595907 AGAGA→GGAGG

- Protein: p.Ile7Thr

- HGVSc: ENST00000335715.9:c.20_24delInsCCTCC

- rsID: —

- Zygosity: Het

- Ref Allele: AGAGA

- Alt Allele: GGAGG

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Not conserved (−0.148)

- Reads: 30

---

  1. TAF3 — Missense variant

- Gene: TAF3

- Variant: COMPLEX 10:7965596 GT→CC

- Protein: p.Val696Pro

- HGVSc: ENST00000344293.6:c.2086_2087delInsCC

- rsID: rs386740632

- Zygosity: Het

- Ref Allele: GT

- Alt Allele: CC

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 2.41)

- Reads: 24

---

  1. TAF4 — Missense variant (Asn60Thr)

- Gene: TAF4

- Variant: SNP 20:62065632 T→G

- Protein: p.Asn60Thr

- HGVSc: ENST00000252996.9:c.179A>C

- rsID: —

- Zygosity: Het

- Ref Allele: T

- Alt Allele: G

- gnomAD genomes v4: 0.0000357 AF · 0.0000783 max ancestry · 5 alt / 139 940 total · 0 hom

- REVEL: 0.016

- Quality: Questionable sequence depth

- Conservation: Highly conserved (phyloP 1.701)

- Reads: 5

---

  1. TAF4 — Missense variant (Gly81Ala)

- Gene: TAF4

- Variant: SNP 20:62065569 C→G

- Protein: p.Gly81Ala

- HGVSc: ENST00000252996.9:c.242G>C

- rsID: —

- Zygosity: Het

- Ref Allele: C

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.044

- Quality: Questionable sequence depth

- Conservation: Marginally conserved (0.055)

- Reads: 6

---

  1. TAF4 — Missense variant (Ser66Thr)

- Gene: TAF4

- Variant: SNP 20:62065614 C→G

- Protein: p.Ser66Thr

- HGVSc: ENST00000252996.9:c.197G>C

- rsID: —

- Zygosity: Het

- Ref Allele: C

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- gnomAD exomes: 0.00000347

- REVEL: 0.023

- Quality: Questionable sequence depth

- Conservation: Moderately conserved (1.419)

- Reads: 6

---

  1. TDG — Splice donor variant

- Gene: TDG

- Variant: SNP 12:103984921 G→A

- Protein: —

- HGVSc: ENST00000392872.8:c.964+1G>A

- rsID: —

- Zygosity: Het

- Ref Allele: G

- Alt Allele: A

- gnomAD genomes v4: 0.00000932 AF · 0.0000191 max ancestry · 1 alt / 107 292 total · 0 hom

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 7.796)

- Reads: 27

---

  1. TET1 — Missense variant

- Gene: TET1

- Variant: COMPLEX 10:68645782 ATA→GTG

- Protein: p.Asn1018_Lys1019delInsSerGlu

- HGVSc: ENST00000373644.5:c.3053_3055delInsGTG

- rsID: rs71483917

- Zygosity: Het

- Ref Allele: ATA

- Alt Allele: GTG

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.245)

- Reads: 36

---

  1. TET2 — Missense variant

- Gene: TET2

- Variant: SNP 4:105234042 C→T

- Protein: p.Leu34Phe

- HGVSc: ENST00000380013.9:c.100C>T

- rsID: rs111948941

- Zygosity: Het

- Ref Allele: C

- Alt Allele: T

- gnomAD genomes v4: 0.0138 AF · 0.0189 max ancestry · 2100 alt / 152 276 total · 30 hom

- ClinVar: Benign

- REVEL: 0.037

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 4.571)

- Reads: 36

---

  1. TRIM24 — Missense variant

- Gene: TRIM24

- Variant: SNP 7:138460706 T→G

- Protein: p.Leu53Trp

- HGVSc: ENST00000343526.9:c.158T>G

- rsID: —

- Zygosity: Het

- Ref Allele: T

- Alt Allele: G

- gnomAD genomes v4: 0.00 AF

- REVEL: 0.542

- Quality: Poor evidence of alternate allele

- Conservation: Highly conserved (phyloP 5.34)

- Reads: 25

---

  1. UGT2B7 — Missense variant (Hom)

- Gene: UGT2B7

- Variant: COMPLEX 4:69098619 AT→TC

- Protein: p.Tyr268His

- HGVSc: ENST00000305231.12:c.801_802delInsTC

- rsID: rs386675647

- Zygosity: Hom (27 alt, 0 ref)

- Ref Allele: AT

- Alt Allele: TC

- gnomAD genomes v4: 0.00 AF

- REVEL: —

- Quality: Sufficient depth and allele counts

- Conservation: Highly conserved (phyloP 2.008)

- Reads: 27

---

  1. UGT2B15 — Missense variant

- Gene: UGT2B15

- Variant: SNP 4:68668134 C→T

- Protein: p.Arg260Gln

reddit.com
u/fondow — 5 days ago
▲ 7 r/DrWillPowers

My VCF gene.iobio.io list

For the BAM variants list, see https://www.reddit.com/r/DrWillPowers/s/jSOrCkJ75S

This will be a very long post of data. A special thank to u/Excellent-Push2833 for all the help. But before, a small AI summary that I suppose must be read with the usual caution.

Summary

CYP2D6 — heterozygous deletion confirmed by BAM (gene depth 19.86 vs flanking 38.93, ratio 0.51). Remaining allele carries *41 markers (rs28371725, rs16947, rs61731586). Genotype: *5/*41 — poor metabolizer. All 10 VCF variants hemizygous (0 ref reads), consistent with single copy.

Top 10 functional variants (VCF-confirmed, genes structurally intact on BAM):

CYP2D6 *5/*41 — poor metabolizer, ~10-25% capacity. Metabolizes ~25% of all prescribed drugs.

UGT2B7 — homozygous *2 (rs7439366, His268Tyr). Primary backup for UGT2B17 glucuronidation.

PAPSS2 — 68/88 variants homozygous ALT (77%). Produces PAPS, the universal cofactor for all sulfotransferases.

DBH — three heterozygous variants: rs1611115 (promoter, reduces expression), rs6271 (Arg549Cys, reduces function), rs1108580 (Ala318Thr). Dopamine-to-norepinephrine conversion impaired.

ABCC2 — two heterozygous loss-of-function variants: rs717620 (promoter) + rs2273697 (Val417Ile). Primary glucuronide efflux transporter.

CYP2C19 — *1/*2 heterozygous (rs4244285 + rs12769205). Intermediate metabolizer.

SLCO2B1 — 12/14 variants homozygous ALT (86%). Sulfated steroid transporter expressed in liver, gut, and brain.

SULT2A1 — 40/45 variants homozygous ALT (89%). Primary androgen sulfation enzyme.

KCNJ8 + ABCC8 — 100% and 78% homozygous ALT respectively. These encode the KATP channel subunits (Kir6.1 + SUR1), the direct pharmacological target of minoxidil. *In my case, penile application of Minoxidil is what made me a severe PFS case, instead of a mild one.*

CREBBP — 53/82 variants homozygous ALT (65%). Histone acetyltransferase and AR coactivator. Dr. Powers has identified CREBBP and NCOR as the most recurrent epigenetic gene findings across PFS and trans genomes.

Supporting findings:

COMT: Val/Val (rs4680 homozygous reference, high activity)

MAO-A: rs6323 T hemizygous (high activity haplotype)

ABCG2: 89% homozygous ALT (drug efflux at blood-brain barrier)

UGT2B15: rare missense p.Arg260Gln (rs371697004, gnomAD AF 0.0000526)

CYP3A5: *1/*3 heterozygous (intermediate metabolizer)

HIF1A: 70% homozygous ALT

SIRT1: 82% homozygous ALT

GCLC: 68% homozygous ALT (glutathione synthesis)

END of AI summary.

BAM deletions :

Deletion/copy-loss hits:

gene chrom start end gene_depth left_depth right_depth flank_mean gene_to_flank_mean gene_to_left gene_to_right call

CYP2D6 22 42126499 42130865 19.8649 40.1108 37.7526 38.9317 0.5103 0.4953 0.5262 POSSIBLE_PARTIAL_OR_HET_DELETION

VCF variants (NOTES/OTHER is also AI) :

Gene: ABCB1

Variant: SNP 7:87549888 T→A

Protein: not displayed (HGVS button not expanded)

rsID: not displayed

Zygosity: Het

Ref Allele: T

Alt Allele: A

Freq: gnomAD genomes v4 — 0.00; gnomAD exomes — 0.0

CADD: not available

REVEL: 0.671

NOTES/OTHER: Missense variant. Sufficient quality. Highly conserved (phyloP 5.04). 0 alt / 0 total in gnomAD. High cross-species conservation.

---

Gene: ABCB8

Variant: SNP 7:151028586 G→A

Protein: p.Arg24His (ENSP00000351717.4)

rsID: rs761485323

Zygosity: Het

Ref Allele: G

Alt Allele: A

Freq: gnomAD genomes v4 — 0.00000657; max ancestry — 0.0000241; gnomAD exomes — 0.00000137

CADD: not available

REVEL: 0.302

NOTES/OTHER: Missense variant. HGVSc: ENST00000358849.9:c.71G>A. Not conserved (phyloP −0.323). 1 alt / 152,240 total. 0 homozygotes.

---

Gene: ABCC5

Variant: SNP 3:183987742 A→T

Protein: intronic in canonical transcript; missense in ENST00000427120

rsID: rs140530675

Zygosity: Het

Ref Allele: A

Alt Allele: T

Freq: gnomAD genomes v4 — 0.000341; max ancestry — 0.000588; gnomAD exomes — 0.000335

CADD: not available

REVEL: not displayed

NOTES/OTHER: Intron variant (canonical transcript ENST00000334444.11:c.591+28T>A). Most severe impact in non-canonical transcript = missense. Marginally conserved (phyloP 0.401). 52 alt / 152,274 total. 1 homozygote.

---

Gene: ARID2

Variant: SNP 12:45905056 A→G

Protein: p.Lys1829Arg (ENSP00000335044.6)

rsID: not displayed

Zygosity: Het

Ref Allele: A

Alt Allele: G

Freq: gnomAD genomes v4 — 0.00; gnomAD exomes — 0.0

CADD: not available

REVEL: 0.023

NOTES/OTHER: Missense variant. HGVSc: ENST00000334344.11:c.5486A>G. Quality: "Poor evidence of alternate allele." Highly conserved (phyloP 2.542). 0 alt / 0 total. Gene-associated phenotypes: severe intellectual disability, generalized hypotonia.

---

Gene: ATP5F1B (variant 1)

Variant: SNP 12:56640166 C→A

Protein: not displayed (HGVS button not expanded)

rsID: not displayed

Zygosity: Het

Ref Allele: C

Alt Allele: A

Freq: gnomAD genomes v4 — 0.00; gnomAD exomes — 0.00

CADD: not available

REVEL: 0.621

NOTES/OTHER: Missense variant. Sufficient quality. Highly conserved (phyloP 9.124). 0 alt / 0 total. Gene-associated phenotypes: hyperleucinemia, hypervalinemia, polyphagia, AD inheritance.

---

Gene: ATP5F1B (variant 2)

Variant: SNP 12:56642557 G→C

Protein: p.Ile325Met (ENSP00000262030.3)

rsID: not displayed

Zygosity: Het

Ref Allele: G

Alt Allele: C

Freq: gnomAD genomes v4 — 0.00; gnomAD exomes — 0.0

CADD: not available

REVEL: 0.501

NOTES/OTHER: Missense variant. HGVSc: ENST00000262030.8:c.975C>G. Sufficient quality. Highly conserved (phyloP 9.129). 0 alt / 0 total. Two heterozygous missense variants on ATP5F1B (possible compound het?).

---

Gene: CAT

Variant: SNP 11:34456041 G→A

Protein: p.Glu248Lys (ENSP00000241052.4)

rsID: not displayed

Zygosity: Het

Ref Allele: G

Alt Allele: A

Freq: gnomAD genomes v4 — 0.00; gnomAD exomes — 0.0

CADD: not available

REVEL: 0.457

NOTES/OTHER: Missense variant. HGVSc: ENST00000241052.5:c.742G>A. Sufficient quality. Highly conserved (phyloP 4.226). 0 alt / 0 total. Gene-associated disease: acatalasemia (AR). Phenotypes: arteriosclerosis, parkinsonism, severe periodontitis.

---

Gene: CHD3

Variant: DEL 17:7884893 CGAG→C

Protein: not displayed (upstream gene variant in canonical; inframe deletion in non-canonical)

rsID: rs770383628

Zygosity: Het

Ref Allele: CGAG

Alt Allele: C

Freq: gnomAD genomes v4 — 0.000322; max ancestry — 0.000845; gnomAD exomes — 0.00694

CADD: not available

REVEL: not displayed

NOTES/OTHER: ClinVar: benign. Upstream gene variant in canonical transcript. Most severe impact in non-canonical transcripts: inframe deletion in ENST00000380358, ENST00000700753. Highly conserved (phyloP 2.282). 45 alt / 139,660 total. 0 homozygotes.

---

Gene: COMT

Variant: SNP 22:19962579 T→A

Protein: p.Leu18Gln (ENSP00000354511.6)

rsID: rs1439513393

Zygosity: Het

Ref Allele: T

Alt Allele: A

Freq: gnomAD genomes v4 — 0.00; gnomAD exomes — 0.00000213

CADD: not available

REVEL: 0.397

NOTES/OTHER: Missense variant. HGVSc: ENST00000361682.11:c.53T>A. Sufficient quality. Not conserved (phyloP −0.518). 0 alt / 0 total (genomes). This variant (p.Leu18Gln) is distinct from rs4680 (Val158Met / Val/Val) which was already documented. Very rare variant in the N-terminal region of COMT. Gene-associated phenotypes: bipolar affective disorder.

---

Gene: CYP21A2

Variant: SNP 6:32041127 G→A

Protein: p.Ser494Asn (ENSP00000496625.1)

rsID: rs6473

Zygosity: Het

Ref Allele: G

Alt Allele: A

Freq: gnomAD genomes v4 — 0.00566; max ancestry — 0.0182; gnomAD exomes — 0.00301

CADD: not available

REVEL: 0.076

NOTES/OTHER: ClinVar: benign (classic congenital adrenal hyperplasia due to 21-hydroxylase deficiency). Missense variant. HGVSc: ENST00000644719.2:c.1481G>A. Marginally conserved (phyloP 0.828). 782 alt / 138,240 total. 0 homozygotes. Phenotype: hypoglycemia.

---

Gene: DBH (variant 1)

Variant: SNP 9:133657152 C→T

Protein: p.Arg549Cys (ENSP00000376776.2)

rsID: rs6271

Zygosity: Het

Ref Allele: C

Alt Allele: T

Freq: gnomAD genomes v4 — 0.0475; max ancestry — 0.0700; gnomAD exomes — 0.0629

CADD: not available

REVEL: 0.182

NOTES/OTHER: ClinVar: benign (orthostatic hypotension 1). Missense variant. HGVSc: ENST00000393056.8:c.1645C>T. Highly conserved (phyloP 3.609). 7,229 alt / 152,278 total. 239 homozygotes. Known functional variant — associated with reduced serum DBH activity.

---

Gene: DBH (variant 2)

Variant: SNP 9:133639992 A→G

Protein: p.Glu162= (synonymous) (ENSP00000376776.2)

rsID: rs1108580

Zygosity: Het

Ref Allele: A

Alt Allele: G

Freq: gnomAD genomes v4 — 0.533; max ancestry — 0.666; gnomAD exomes — 0.515

CADD: not available

REVEL: not applicable (synonymous)

NOTES/OTHER: ClinVar: benign (orthostatic hypotension 1). Splice region variant + synonymous variant. HGVSc: ENST00000393056.8:c.486A>G. Highly conserved (phyloP 9.321). 80,984 alt / 152,062 total. 22,686 homozygotes. Common variant, but splice region positioning confers functional interest.

---

Gene: DBH (variant 3)

Variant: SNP 9:133635393 T→C

Protein: not applicable (upstream gene variant)

rsID: rs1611115

Zygosity: Het

Ref Allele: T

Alt Allele: C

Freq: gnomAD genomes v4 — 0.796; max ancestry — 0.829; gnomAD exomes — 0.0

CADD: not available

REVEL: not applicable

NOTES/OTHER: ClinVar: "Not provided" (orthostatic hypotension 1). Upstream gene variant (promoter). Not conserved (phyloP −0.298). 120,899 alt / 151,818 total. 48,324 homozygotes. Known −1021C>T variant — the C allele (alt) is a major negative regulator of DBH expression, associated with reduced plasma DBH activity.

---

Gene: DRD4

Variant: SNP 11:640099 A→C

Protein: p.Ser284Arg (ENSP00000176183.5)

rsID: rs34662058

Zygosity: Het

Ref Allele: A

Alt Allele: C

Freq: gnomAD genomes v4 — 0.000572; max ancestry — 0.00439; gnomAD exomes — 0.000803

CADD: not available

REVEL: 0.043

NOTES/OTHER: Missense variant. HGVSc: ENST00000176183.6:c.850A>C. Sufficient quality. Not conserved (phyloP −1.067). 55 alt / 96,084 total. 2 homozygotes. Gene-associated phenotype: hyperactivity.

---

Gene: HDAC9

Variant: SNP 7:18954219 T→C

Protein: p.Ile1004Thr (ENSP00000509161.1)

rsID: rs138163349

Zygosity: Het

Ref Allele: T

Alt Allele: C

Freq: gnomAD genomes v4 — 0.00209; max ancestry — 0.00334; gnomAD exomes — 0.00256

CADD: not available

REVEL: 0.051

NOTES/OTHER: ClinVar: benign (not provided). Missense variant. HGVSc: ENST00000886413.1:c.3011T>C. Marginally conserved (phyloP 0.848). 318 alt / 152,234 total. 4 homozygotes.

---

Gene: HTR1D

Variant: SNP 1:23193766 C→A

Protein: p.Ala152Ser (ENSP00000363748.1)

rsID: rs142643700

Zygosity: Het

Ref Allele: C

Alt Allele: A

Freq: gnomAD genomes v4 — 0.000440; max ancestry — 0.000544; gnomAD exomes — 0.000441

CADD: not available

REVEL: 0.121

NOTES/OTHER: ClinVar: uncertain significance (VUS). Missense variant. HGVSc: ENST00000374619.2:c.454G>T. Sufficient quality. Not conserved (phyloP −3.894). 67 alt / 152,202 total. 0 homozygotes. Serotonin receptor 1D.

---

Gene: KAT6B

Variant: SNP 10:74843533 G→A

Protein: intronic in canonical; missense in ENST00000648539, ENST00000650434

rsID: rs138782403

Zygosity: Het

Ref Allele: G

Alt Allele: A

Freq: gnomAD genomes v4 — 0.0104; max ancestry — 0.0175; gnomAD exomes — 0.0152

CADD: not available

REVEL: not displayed

NOTES/OTHER: ClinVar: likely benign (not provided). Intron variant (ENST00000287239.10:c.621+55G>A). Marginally conserved (phyloP 0.469). 1,591 alt / 152,290 total. 8 homozygotes. Gene-associated disease: genitopatellar syndrome (AD).

---

Gene: KDM6B

Variant: SNP 17:7853303 G→T

Protein: p.Ala1611Ser (ENSP00000412513.2)

rsID: rs141627015

Zygosity: Het

Ref Allele: G

Alt Allele: T

Freq: gnomAD genomes v4 — 0.0000591; max ancestry — 0.000118; gnomAD exomes — 0.0000788

CADD: not available

REVEL: 0.071

NOTES/OTHER: ClinVar: likely benign (inborn genetic diseases). Missense variant. HGVSc: ENST00000448097.7:c.4831G>T. Moderately conserved (phyloP 1.113). 9 alt / 152,324 total. 0 homozygotes. Gene-associated phenotypes: epilepsy, motor delay, hypotonia, global developmental delay.

---

Gene: MFN2

Variant: SNP 1:12014474 A→G

Protein: downstream gene variant in canonical; missense in ENST00000675298

rsID: rs143440477

Zygosity: Het

Ref Allele: A

Alt Allele: G

Freq: gnomAD genomes v4 — 0.00280; max ancestry — 0.00550; gnomAD exomes — 0.0

CADD: not available

REVEL: not displayed

NOTES/OTHER: ClinVar: likely benign (not provided). Downstream gene variant in canonical transcript. Not conserved (phyloP −0.765). 401 alt / 143,404 total. 2 homozygotes. Gene involved in mitochondrial fusion.

---

Gene: MT-ATP6

Variant: SNP MT:8860 A→G

Protein: p.Thr112Ala (ENSP00000354632.2)

rsID: rs2001031

Zygosity: Hom

Ref Allele: A

Alt Allele: G

Freq: gnomAD genomes v4 — 249 alt, 0 ref (near-fixed)

CADD: not available

REVEL: not displayed

NOTES/OTHER: ClinVar: benign (Leigh syndrome). Mitochondrial missense variant. HGVSc: ENST00000361899.2:c.334A>G. Highly conserved (phyloP 3.819). Near-fixed mitochondrial DNA variant — constitutes the revised Cambridge Reference Sequence (rCRS) polymorphism. Gene-associated diseases: Leber hereditary optic neuropathy, NARP syndrome, familial isolated hypertrophic cardiomyopathy, isolated ATP synthase deficiency.

---

Gene: MT-CYB

Variant: SNP MT:15326 A→G

Protein: p.Thr194Ala (ENSP00000354554.2)

rsID: rs2853508

Zygosity: Hom

Ref Allele: A

Alt Allele: G

Freq: gnomAD genomes v4 — 248 alt, 0 ref (near-fixed)

CADD: not available

REVEL: not displayed

NOTES/OTHER: ClinVar: benign (Leigh syndrome, mitochondrial disease, familial breast cancer). Mitochondrial missense variant. HGVSc: ENST00000361789.2:c.580A>G. Marginally conserved (phyloP 0.228). Like MT-ATP6 rs2001031, near-fixed variant — rCRS polymorphism.

---

Gene: NSD1

Variant: SNP 5:177212121 G→C

Protein: p.Ser1241Thr (ENSP00000395929.2)

rsID: rs138641637

Zygosity: Het

Ref Allele: G

Alt Allele: C

Freq: gnomAD genomes v4 — 0.000670; max ancestry — 0.00308; gnomAD exomes — 0.000761

CADD: not available

REVEL: 0.049

NOTES/OTHER: ClinVar: likely benign (Sotos syndrome, Weaver syndrome, inborn genetic diseases). Missense variant. HGVSc: ENST00000439151.7:c.3722G>C. Not conserved (phyloP −0.071). 102 alt / 152,134 total. 0 homozygotes.

---

Gene: SLC22A13

Variant: SNP 3:38275953 C→T

Protein: p.Thr365Met (ENSP00000310241.3)

rsID: rs765934579

Zygosity: Het

Ref Allele: C

Alt Allele: T

Freq: gnomAD genomes v4 — 0.0000394; max ancestry — 0.000576; gnomAD exomes — 0.0000315

CADD: not available

REVEL: 0.376

NOTES/OTHER: Missense variant. HGVSc: ENST00000311856.9:c.1094C>T. Sufficient quality. Not conserved (phyloP −5.666). 6 alt / 152,224 total. 0 homozygotes. Organic cation transporter — relevant to renal clearance of endogenous substrates.

---

Gene: SLCO3A1

Variant: SNP 15:92104454 A→C

Protein: p.Arg307Ser (ENSP00000320634.6)

rsID: rs72655652

Zygosity: Het

Ref Allele: A

Alt Allele: C

Freq: gnomAD genomes v4 — 0.0115; max ancestry — 0.0168; gnomAD exomes — 0.0139

CADD: not available

REVEL: 0.086

NOTES/OTHER: Missense variant. HGVSc: ENST00000318445.11:c.921A>C. Sufficient quality. Highly conserved (phyloP 6.031). 1,758 alt / 152,250 total. 19 homozygotes. OATP family transporter — potentially relevant for conjugated steroid transport.

---

Gene: SOD2

Variant: SNP 6:159692745 G→C

Protein: not displayed (HGVS button not expanded)

rsID: not displayed

Zygosity: Het

Ref Allele: G

Alt Allele: C

Freq: gnomAD genomes v4 — 0.00; gnomAD exomes — 6.84e-7

CADD: not available

REVEL: 0.083

NOTES/OTHER: Missense variant. Sufficient quality. Highly conserved (phyloP 7.494). 0 alt / 152,186 total. 0 homozygotes. Extremely rare variant on mitochondrial superoxide dismutase.

---

Gene: STAT3

Variant: SNP 17:42329523 C→T

Protein: intronic in canonical; missense in ENST00000677421

rsID: rs112644937

Zygosity: Het

Ref Allele: C

Alt Allele: T

Freq: gnomAD genomes v4 — 0.00121; max ancestry — 0.00307; gnomAD exomes — 0.00151

CADD: not available

REVEL: not displayed

NOTES/OTHER: ClinVar: likely benign (not provided). Intron variant (ENST00000264657.10:c.1233+31G>A). Marginally conserved (phyloP 0.629). 185 alt / 152,328 total. 0 homozygotes. Gene-associated diseases: acute promyelocytic leukemia, chronic lymphoproliferative disorder of natural killer cells.

---

Gene: TBP

Variant: DEL 6:170561958 ACAG→A

Protein: p.Gln95del (ENSP00000375942.2)

rsID: rs752404282

Zygosity: Het

Ref Allele: ACAG

Alt Allele: A

Freq: gnomAD genomes v4 — 0.00403; max ancestry — 0.00513; gnomAD exomes — 0.00574

CADD: not available

REVEL: not applicable (inframe deletion)

NOTES/OTHER: ClinVar: benign. Inframe deletion. HGVSc: ENST00000392092.7:c.279_281del. Marginally conserved (phyloP 0.29). 578 alt / 143,364 total. 4 homozygotes. Gene-associated phenotype: cerebellar atrophy.

---

Gene: TET2

Variant: SNP 4:105234042 C→T

Protein: p.Leu34Phe (ENSP00000369351.4)

rsID: rs111948941

Zygosity: Het

Ref Allele: C

Alt Allele: T

Freq: gnomAD genomes v4 — 0.0138; max ancestry — 0.0189; gnomAD exomes — not displayed

CADD: not available

REVEL: 0.037

NOTES/OTHER: ClinVar: benign (not provided). Missense variant. HGVSc: ENST00000380013.9:c.100C>T. Highly conserved (phyloP 4.571). 2,100 alt / 152,276 total. 30 homozygotes. Gene-associated diseases: primary myelofibrosis, polycythemia vera, acquired idiopathic sideroblastic anemia.

---

Gene: UGT2B15

Variant: SNP 4:68868134 C→T

Protein: p.Arg260Gln (ENSP00000341045.5)

rsID: rs371697004

Zygosity: Het

Ref Allele: C

Alt Allele: T

Freq: gnomAD genomes v4 — 0.0000526; max ancestry — 0.0000735; gnomAD exomes — 0.0000322

CADD: not available

REVEL: 0.307

NOTES/OTHER: Missense variant. HGVSc: ENST00000338206.6:c.779G>A. Sufficient quality. Marginally conserved (phyloP 0.443). 8 alt / 152,046 total. 0 homozygotes. Androgenic glucuronidation enzyme — directly relevant to androgen metabolite clearance (UGT2B cascade).

---

Structural Variants / CNV (Transcript Ablation / Amplification)

---

Gene: ABCC1

Variant: Transcript ablation (CNV)

Protein: not applicable

rsID: not applicable

Zygosity: indeterminate (structural)

Ref Allele: not applicable

Alt Allele: deletion / ablation

Freq: not displayed

CADD: not available

REVEL: not applicable

NOTES/OTHER: chr16:15,949,138–16,143,257. Aliases: GS-X, MRP, MRP1. MANE transcript: ENST00000399410.8. 1 variant identified (proband). Classified under "High or moderate impact" as transcript ablation. Phenotypes: AD sensorineural deafness (DFNA), tinnitus, morphological abnormality of the inner ear. ABC transporter — exports glutathione, glucuronide, and sulfate conjugates. Directly relevant to conjugated androgen clearance (ABCC2 was already documented in the PFS profile).

---

Gene: CYP2E1

Variant: Transcript amplification (CNV)

Protein: not applicable

rsID: not applicable

Zygosity: indeterminate (structural)

Ref Allele: not applicable

Alt Allele: amplification

Freq: not displayed

CADD: not available

REVEL: not applicable

NOTES/OTHER: chr10:133,520,406–133,561,220. Alias: CYP2E. MANE transcript: ENST00000252945.8. 1 variant identified (proband). Classified under "High or moderate impact" as transcript amplification. CYP2E1 metabolizes ethanol, fatty acids, and certain xenobiotics; amplification could increase phase I metabolic activity through this CYP.

---

Gene: GUSB

Variant: Transcript amplification (CNV)

Protein: not applicable

rsID: not applicable

Zygosity: indeterminate (structural)

Ref Allele: not applicable

Alt Allele: amplification

Freq: not displayed

CADD: not available

REVEL: not applicable

NOTES/OTHER: chr7:65,960,684–65,982,215 (reverse strand). MANE transcript: ENST00000304895.9. 0 point variants identified. Classified under "High or moderate impact" as transcript amplification. Lysosomal β-glucuronidase — catalyzes hydrolysis of glucuronides. Potential relevance: increased GUSB activity could prematurely deconjugate glucuronidated androgens (DHT-G, 3α-ADG), partially counteracting UGT2B function.

---

Gene: HDAC1

Variant: Transcript amplification (CNV)

Protein: not applicable

rsID: not applicable

Zygosity: indeterminate (structural)

Ref Allele: not applicable

Alt Allele: amplification

Freq: not displayed

CADD: not available

REVEL: not applicable

NOTES/OTHER: chr1:32,292,083–32,333,635. Aliases: GON-10, HD1, KDAC1, RPD3L1. MANE transcript: ENST00000373548.8. 0 point variants identified. Classified under "High or moderate impact" as transcript amplification. Class I histone deacetylase — epigenetic regulator. Finasteride and other endocrine disruptors are known to alter histone acetylation patterns; HDAC1 amplification could potentiate persistent epigenetic repression in the PFS context.

---

IGV View — CYP2D6

---

Gene: CYP2D6

Variant: IGV visual inspection

Protein: not applicable (coverage inspection)

rsID: not applicable

Zygosity: indeterminate

Ref Allele: not applicable

Alt Allele: not applicable

Freq: not applicable

CADD: not applicable

REVEL: not applicable

NOTES/OTHER: IGV capture of the chr22:42,124,499–42,132,810 region (GRCh38). BAM file (sample.bam) loaded with coverage and aligned reads. Coverage appears variable with some reduced-depth regions. Some colored reads (red, green, purple) suggesting soft-clips or mismatches — to be evaluated for potential structural rearrangements (CYP2D6 is known for duplications/deletions/CYP2D6-CYP2D7 hybrids). The Powers subreddit CNV script had already flagged CYP2D6 as potentially abnormal.

---

- HGVSc: ENST00000338206.6:c.779G>A

- rsID: rs371697004

- Zygosity: Het

- Ref Allele: C

- Alt Allele: T

- gnomAD genomes v4: 0.0000526 AF · 0.0000735 max ancestry · 8 alt / 152 046 total · 0 hom

- REVEL: 0.307

- Quality: Sufficient depth and allele counts

- Conservation: Marginally conserved (0.443)

- Reads: 49

reddit.com
u/fondow — 5 days ago
▲ 5 r/PikaOS

I recently tried to install PikaOS and was surprised to be presented with an EULA that one is required to accept.

Any real EULA, or in other words, a contract whose acceptance conditions the user's ability to run, install, or modify the software would, as regards the GPL-licensed components of PikaOS, constitute a "further restriction on the recipients' exercise of the rights granted" within the meaning of the GPL (s. 10 for v2 or 10 for v3). As such, it would be unenforceable. To the extent the "EULA" purports to restrict, it contradicts the upstream licenses and is void. To the extent it does not purport to restrict, it is not an EULA at all, but more like a notice wearing the wrong name.

The eight items listed in it (note about Debian's trademark, a disclaimer that PikaOS is a hobby project, a reminder not to interrupt the installer, a suggestion to use pikman over apt, the default session credentials, etc.) are, without exception, factual notices and practical tips. There are no obligations, no restrictions, no grants of rights, no real limitations of liability. Point 8 literally reads "password: [blank] — MEANING: JUST PRESS ENTER". This is a (useful) README, not a contract. Why, then, call it an EULA when a simple "warning" or "notice" would suffice as it is clearly the case for PikaOS?

I am aware that Firefox (mostly on Windows) has recently adopted a similar practice. However, is not an argument. Mozilla can inform users that the distributed build ships with telemetry, that crash reports may be transmitted, and so on. But what is presented in such screens as "Terms of Use" or "EULA" is not, in substance, a set of enforceable restrictions on the execution or use of the program. So long as they do not condition or restrict the user's ability to run or modify the software, they function as informational notices about how the distributed version operates. This can be useful. It is not, however, the function of an EULA or "Terms of Use", and it should not be named as one.

FOSS distributions should never present an EULA, and users of FOSS should never be required to read or agree to a "license" merely in order to run or install a computer program. The FOSS licenses (GPL, MIT, Apache, etc.) already grant the necessary rights to every recipient, unconditionally and without any further act of acceptance. Acceptance is triggered only when the user engages in acts of redistribution or modification that would otherwise infringe copyright. The GPL operates as a unilateral grant, not as a contract of adhesion the user must sign before running the program.

The same is, in fact, true of proprietary software. The idea that one must agree to an EULA in order to run or install a program one has lawfully acquired is a myth. Many proprietary software were in the past distributed without any EULA, and some are still are.

In the case of PikaOS, the solution is simple. Instead of calling this screen an EULA (which is not), just call it a "notice", "disclosure", or “warning”. The substance of your communication can stay exactly as it is.

I realize that I might be the only one to care about that, and I hope that I’m not bothering people here too much. It’s just that I spent several years writing a doctoral thesis in software law.

Thank you!

Oh... In a totally different matter. Canadian French does not appear to be available as a keyboard layout/installer language. We use a QWERTY layout with a few differences for French characters. The common “French” from France AZERTY is foreign to us. This is the first Linux distribution I've seen that does not offer it. In fact, no Canadian layout, neither English nor French, appears anywhere. Typing "cana" in the search box returns only Inupiaq. Can it be an issue this particular installer that PikaOS is using?

EDIT: I went further in the installation process, and French Canada is available, just not on the first language selection screen.

reddit.com
u/fondow — 2 months ago