ClinVar Miner

Submissions for variant NM_001018115.3(FANCD2):c.990-1G>A

gnomAD frequency: 0.00005  dbSNP: rs112832879
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000421802 SCV000520943 likely pathogenic not provided 2022-07-31 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 23613520, 17436244)
Fulgent Genetics, Fulgent Genetics RCV001535895 SCV001752528 pathogenic Fanconi anemia complementation group D2 2021-06-30 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV002256229 SCV002531768 pathogenic Fanconi anemia 2021-11-18 criteria provided, single submitter curation
Baylor Genetics RCV001535895 SCV004196736 pathogenic Fanconi anemia complementation group D2 2023-08-18 criteria provided, single submitter clinical testing
Invitae RCV002256229 SCV004370426 pathogenic Fanconi anemia 2024-01-31 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 12 of the FANCD2 gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. Disruption of this splice site has been observed in individual(s) with Fanconi anemia (PMID: 17436244, 23613520). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as IVS12-1G>A. ClinVar contains an entry for this variant (Variation ID: 381559). Studies have shown that disruption of this splice site results in activation of a cryptic splice acceptor and introduces a premature termination codon (PMID: 17436244). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic.
Sung Lab, Department of Medicine, Roswell Park Comprehensive Cancer Center RCV003234557 SCV003932622 pathogenic Acute myeloid leukemia 2023-06-08 no assertion criteria provided clinical testing

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