ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.3263C>T (p.Ser1088Phe)

gnomAD frequency: 0.05303  dbSNP: rs17233497
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Preventiongenetics, part of Exact Sciences RCV000120937 SCV000302488 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001094408 SCV000399830 benign Fanconi anemia complementation group A 2018-03-06 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.
Invitae RCV000351747 SCV000558864 benign Fanconi anemia 2024-02-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000120937 SCV000603544 benign not specified 2016-10-06 criteria provided, single submitter clinical testing
GeneDx RCV001705888 SCV001900776 benign not provided 2019-03-12 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 31586946, 28864460, 10094191, 27153395, 27884173, 24728327, 20981092, 22995991)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000120937 SCV002051221 benign not specified 2021-12-18 criteria provided, single submitter clinical testing Variant summary: FANCA c.3263C>T (p.Ser1088Phe) 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 0.051 in 250776 control chromosomes in the gnomAD database, including 459 homozygotes. The observed variant frequency is approximately 23.34 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. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments. Based on the evidence outlined above, the variant was classified as benign.
Sema4, Sema4 RCV000351747 SCV002534994 benign Fanconi anemia 2020-02-06 criteria provided, single submitter curation
ITMI RCV000120937 SCV000085105 not provided not specified 2013-09-19 no assertion provided reference population
Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine RCV000488415 SCV000494044 uncertain significance Malignant tumor of prostate 2015-07-01 flagged submission research
Leiden Open Variation Database RCV001094408 SCV001426104 pathogenic Fanconi anemia complementation group A 2020-02-28 flagged submission curation Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.
Natera, Inc. RCV001094408 SCV001458821 benign Fanconi anemia complementation group A 2019-08-23 no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000120937 SCV001927758 benign not specified no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000120937 SCV001963397 benign not specified no assertion criteria provided clinical testing

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