ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.1901-3C>A

dbSNP: rs17226526
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001094419 SCV000399854 likely benign Fanconi anemia complementation group A 2018-01-12 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae RCV000259319 SCV000960817 likely benign Fanconi anemia 2024-01-31 criteria provided, single submitter clinical testing
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV000259319 SCV001737430 uncertain significance Fanconi anemia 2021-06-10 criteria provided, single submitter clinical testing The FANCA c.1901-3C>A intronic change results in a C to A substitution at the -3 position of intron 21 of the FANCA gene. This variant is not predicted to affect the native splice acceptor site (BP4), but to our knowledge these predictions have not been confirmed by functional assays. This variant has a maximum subpopulation frequency of 0.097% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/16-89839795-G-T?dataset=gnomad_r2_1). To our knowledge, this variant has not been reported in individuals with Fanconi anemia. In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: BP4.
Baylor Genetics RCV001094419 SCV002030121 uncertain significance Fanconi anemia complementation group A 2021-06-29 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Natera, Inc. RCV001094419 SCV001462950 uncertain significance Fanconi anemia complementation group A 2019-10-28 no assertion criteria provided clinical testing

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