ClinVar Miner

Submissions for variant NM_144670.6(A2ML1):c.3269G>A (p.Gly1090Asp)

gnomAD frequency: 0.00080  dbSNP: rs200964353
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000228261 SCV000291410 likely benign not provided 2025-01-28 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001194017 SCV001363248 benign not specified 2019-12-09 criteria provided, single submitter clinical testing Variant summary: A2ML1 c.3269G>A (p.Gly1090Asp) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00069 in 249556 control chromosomes, predominantly at a frequency of 0.0013 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 325 fold of the estimated maximal expected allele frequency for a pathogenic variant in A2ML1 causing Noonan Syndrome phenotype (4e-06), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. A ClinVar submission (evaluation after 2014) cites the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV000228261 SCV001836705 benign not provided 2019-05-30 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000228261 SCV001744768 likely benign not provided no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000228261 SCV001951720 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV001194017 SCV002034543 benign not specified no assertion criteria provided clinical testing

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