ClinVar Miner

Submissions for variant NM_000135.4(FANCA):c.4261-2A>C

dbSNP: rs915983602
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000656368 SCV000793846 pathogenic Fanconi anemia complementation group A 2017-09-01 criteria provided, single submitter clinical testing
Invitae RCV001855345 SCV002237767 pathogenic Fanconi anemia 2023-11-27 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 42 of the FANCA gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product. This variant is present in population databases (no rsID available, gnomAD 0.0009%). Disruption of this splice site has been observed in individual(s) with Fanconi anemia (PMID: 15059067, 27041517, 28060124, 29098742; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is also known as IVS42-2A>C. ClinVar contains an entry for this variant (Variation ID: 545114). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000656368 SCV004196601 pathogenic Fanconi anemia complementation group A 2022-12-19 criteria provided, single submitter clinical testing
Department of Pathology and Genetics, University of Gothenburg RCV000656368 SCV000777898 likely pathogenic Fanconi anemia complementation group A 2017-01-01 no assertion criteria provided clinical testing
Department of Pathology and Genetics, University of Gothenburg RCV000656370 SCV000777900 uncertain significance Neuroblastoma 2017-01-01 flagged submission clinical testing

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