ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.3982A>G (p.Thr1328Ala)

gnomAD frequency: 0.05868  dbSNP: rs9282681
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000120951 SCV000302500 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001094348 SCV000399812 benign Fanconi anemia complementation group A 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000120951 SCV000603552 benign not specified 2016-10-06 criteria provided, single submitter clinical testing
Invitae RCV000311773 SCV001000427 benign Fanconi anemia 2024-02-01 criteria provided, single submitter clinical testing
GeneDx RCV001705889 SCV001857880 benign not provided 2019-03-12 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 31586946, 9371798, 27121516)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000120951 SCV002051223 benign not specified 2021-12-18 criteria provided, single submitter clinical testing Variant summary: FANCA c.3982A>G (p.Thr1328Ala) results in a non-conservative amino acid change in the encoded protein sequence. Two of three in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.066 in 156058 control chromosomes in the gnomAD database, including 617 homozygotes. The observed variant frequency is approximately 30.55 fold of the estimated maximal expected allele frequency for a pathogenic variant in FANCA causing Fanconi Anemia phenotype (0.0022), strongly suggesting that the variant is benign. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Five classified the variant as benign while one classified as pathogenic. Based on the evidence outlined above, the variant was classified as benign.
ITMI RCV000120951 SCV000085119 not provided not specified 2013-09-19 no assertion provided reference population
Leiden Open Variation Database RCV001094348 SCV001426131 pathogenic Fanconi anemia complementation group A 2020-02-28 flagged submission curation Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.
Natera, Inc. RCV001094348 SCV001457774 benign Fanconi anemia complementation group A 2019-08-23 no assertion criteria provided clinical testing

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