ClinVar Miner

Submissions for variant NM_153704.6(TMEM67):c.43T>A (p.Ser15Thr)

gnomAD frequency: 0.00008  dbSNP: rs748221725
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001193312 SCV001362063 uncertain significance not specified 2020-08-19 criteria provided, single submitter clinical testing Variant summary: TMEM67 c.43T>A (p.Ser15Thr) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 8.4e-05 in 251436 control chromosomes, predominantly at a frequency of 0.00061 within the Latino subpopulation in the gnomAD database. This frequency is lower than the estimated maximum allele frequency expected for a pathogenic variant in TMEM67 causing Joubert Syndrome 6 (0.00061 vs 0.004), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.43T>A in individuals affected with Joubert Syndrome 6 and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as uncertain significance.
Fulgent Genetics, Fulgent Genetics RCV002480641 SCV002791775 uncertain significance COACH syndrome 1; Joubert syndrome 6; Meckel syndrome, type 3; RHYNS syndrome; Bardet-Biedl syndrome 14; Nephronophthisis 11 2021-09-20 criteria provided, single submitter clinical testing
Invitae RCV002561008 SCV003026845 likely benign Familial aplasia of the vermis; Meckel-Gruber syndrome 2023-09-12 criteria provided, single submitter clinical testing

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