ClinVar Miner

Submissions for variant NM_000091.5(COL4A3):c.3031C>T (p.Arg1011Cys)

gnomAD frequency: 0.00233  dbSNP: rs73996408
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000252602 SCV000302069 benign not specified criteria provided, single submitter clinical testing
GeneDx RCV000840151 SCV000982068 benign not provided 2020-02-04 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000840151 SCV001062779 benign not provided 2025-01-31 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000252602 SCV002500526 benign not specified 2022-03-20 criteria provided, single submitter clinical testing Variant summary: COL4A3 c.3031C>T (p.Arg1011Cys) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00055 in 249538 control chromosomes, predominantly at a frequency of 0.0077 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 4 fold of the estimated maximal expected allele frequency for a pathogenic variant in COL4A3 causing Alport Syndrome, Autosomal Recessive phenotype (0.0019), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. To our knowledge, no penetrant association c.3031C>T in individuals affected with Alport Syndrome, Autosomal Recessive and no experimental evidence demonstrating its impact on protein function have been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Natera, Inc. RCV001833254 SCV002076413 likely benign Alport syndrome 2021-06-08 no assertion criteria provided clinical testing

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