ClinVar Miner

Submissions for variant NM_004629.2(FANCG):c.1538G>A (p.Arg513Gln)

gnomAD frequency: 0.00863  dbSNP: rs17885240
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Total submissions: 18
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000229666 SCV000288623 benign Fanconi anemia 2024-02-01 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003891643 SCV000310551 benign FANCG-related disorder 2019-10-09 criteria provided, single submitter clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Illumina Laboratory Services, Illumina RCV000317116 SCV000484369 likely benign Inclusion Body Myopathy, Dominant 2016-06-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000353275 SCV000484370 likely benign Amyotrophic Lateral Sclerosis, Dominant 2016-06-14 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000121035 SCV000594705 benign not specified 2016-11-14 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001168311 SCV001330891 uncertain significance Fanconi anemia complementation group G 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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Genome-Nilou Lab RCV001168311 SCV001653325 likely benign Fanconi anemia complementation group G 2021-05-18 criteria provided, single submitter clinical testing
GeneDx RCV001194965 SCV001834775 likely benign not provided 2020-10-08 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 26033879, 12552564, 16643430)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000121035 SCV003844910 benign not specified 2023-02-17 criteria provided, single submitter clinical testing Variant summary: FANCG c.1538G>A (p.Arg513Gln) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0083 in 251472 control chromosomes in the gnomAD database, including 14 homozygotes. The observed variant frequency is approximately 9.41 fold of the estimated maximal expected allele frequency for a pathogenic variant in FANCG causing Fanconi Anemia phenotype (0.00088), strongly suggesting that the variant is benign. c.1538G>A has been reported in the literature in individuals affected with Fanconi Anemia and Acute Myeloid Leukemia (e.g., Meyer_2006, Nicchia_2015) however without strong evidence for causality. These reports therefore do not provide conclusions about association of the variant with Fanconi Anemia. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Eight ClinVar submitters (evaluation after 2014) have reported the variant with conflicting assessments: three cite the variant as benign, three cite the variant as likely benign, one cites the variant as uncertain signficance, and one cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as benign.
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV001168311 SCV004017686 benign Fanconi anemia complementation group G 2023-07-07 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001194965 SCV004157696 benign not provided 2024-04-01 criteria provided, single submitter clinical testing FANCG: BP4, BS1, BS2
Molecular Genetics, Royal Melbourne Hospital RCV001168311 SCV004812750 benign Fanconi anemia complementation group G 2024-01-05 criteria provided, single submitter clinical testing
ITMI RCV000121035 SCV000085203 not provided not specified 2013-09-19 no assertion provided reference population
Leiden Open Variation Database RCV001194965 SCV001364839 pathogenic not provided 2020-02-28 no assertion criteria provided curation Curator: Arleen D. Auerbach. Submitter to LOVD: Johan de Winter.
Natera, Inc. RCV001168311 SCV001452297 benign Fanconi anemia complementation group G 2020-09-16 no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000121035 SCV001809787 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000121035 SCV001931526 benign not specified no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001194965 SCV002036805 likely benign not provided no assertion criteria provided clinical testing

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