Two VUS variants found in the same gene during exome sequencing how do geneticists think about whether this is meaningful or coincidental?
I'm trying to understand something about how genetic variant interpretation works and would love input from people who understand this better than I do.
A proband had whole exome sequencing.
Two heterozygous variants of uncertain significance were found in the same gene. The proband's clinical features somewhat overlap with the published phenotype for that syndrome. Parental testing has not been done yet.
I have a few questions about the genetics reasoning here, not asking anyone to interpret specific results:
Question 1:
What are the odds that two VUS variants land in the same gene purely by coincidence during exome sequencing? Is finding two variants in the same gene more meaningful than finding one, statistically speaking?
Question 2:
Before parental testing is done, what is the starting probability that two VUS in that gene actually represent a true genetic finding, versus just being noise? Do geneticists have a way of thinking through this?
Question 3:
How much weight do clinical geneticists give to the fact that the person's clinical features overlap with the published phenotype for that gene? Does a strong phenotype match move the needle on how seriously to take a VUS in that gene?
Thanks in advance.