ClinVar Miner

Submissions for variant NM_001018115.3(FANCD2):c.1367T>G (p.Leu456Arg)

gnomAD frequency: 0.02918  dbSNP: rs35782247
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Total submissions: 14
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000120985 SCV000305857 likely benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001094941 SCV000439476 likely benign Fanconi anemia complementation group D2 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000434788 SCV000511003 benign not provided 2016-12-14 criteria provided, single submitter clinical testing
Invitae RCV000406228 SCV000558538 benign Fanconi anemia 2023-12-07 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000120985 SCV000603570 benign not specified 2017-03-29 criteria provided, single submitter clinical testing
GeneDx RCV000434788 SCV001849301 benign not provided 2019-04-25 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 21356188, 27153395, 24728327, 20981092, 17436244)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000120985 SCV002051296 benign not specified 2021-12-20 criteria provided, single submitter clinical testing Variant summary: FANCD2 c.1367T>G (p.Leu456Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.007 in 251396 control chromosomes, predominantly at a frequency of 0.099 within the African or African-American subpopulation in the gnomAD database, including 2 homozygotes. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 204.49 fold of the estimated maximal expected allele frequency for a pathogenic variant in FANCD2 causing Fanconi Anemia phenotype (0.00048), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, with conflicting interpretation. Based on the evidence outlined above, the variant was classified as benign.
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State RCV002225375 SCV002505198 benign Hereditary breast ovarian cancer syndrome 2022-04-19 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000406228 SCV002529457 benign Fanconi anemia 2020-09-10 criteria provided, single submitter curation
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV001094941 SCV004017642 benign Fanconi anemia complementation group D2 2023-07-07 criteria provided, single submitter clinical testing
ITMI RCV000120985 SCV000085153 not provided not specified 2013-09-19 no assertion provided reference population
Leiden Open Variation Database RCV001094941 SCV001364780 pathogenic Fanconi anemia complementation group D2 2020-02-28 flagged submission curation Curator: Arleen D. Auerbach. Submitter to LOVD: Arleen D. Auerbach.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000434788 SCV001800169 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000120985 SCV001807258 benign not specified no assertion criteria provided clinical testing

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