ClinVar Miner

Submissions for variant NM_020937.4(FANCM):c.624A>G (p.Ile208Met)

gnomAD frequency: 0.01077  dbSNP: rs45547534
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000230015 SCV000290520 benign Fanconi anemia 2024-02-01 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000506045 SCV000603598 benign not specified 2017-02-17 criteria provided, single submitter clinical testing
GeneDx RCV001548048 SCV001767897 likely benign not provided 2021-03-21 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000506045 SCV002046720 benign not specified 2021-03-16 criteria provided, single submitter clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center RCV003316301 SCV004015695 benign Premature ovarian failure 15 2023-07-07 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001548048 SCV004042585 benign not provided 2024-04-01 criteria provided, single submitter clinical testing FANCM: BP4, BS1, BS2
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000506045 SCV001553788 benign not specified no assertion criteria provided clinical testing The FANCM p.Ile208Met variant was identified in 6 of 854 proband chromosomes (frequency: 0.007) from individuals with breast or ovarian cancer (Nguyen-Dumont_2018_PMID:29351780). The variant was identified in dbSNP (ID: rs45547534) and ClinVar (classified as benign by ARUP Laboratories and Invitae). The variant was not identified in the Cosmic database and in control databases in 2619 of 268068 chromosomes (22 homozygous) at a frequency of 0.00977 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database March 6, 2019, v2.1.1). The variant was observed in the following populations: European (non-Finnish) in 1778 of 118106 chromosomes (freq: 0.01505), South Asian in 313 of 30522 chromosomes (freq: 0.01025), Other in 63 of 6702 chromosomes (freq: 0.0094), Latino in 237 of 35106 chromosomes (freq: 0.006751), European (Finnish) in 136 of 24908 chromosomes (freq: 0.00546), Ashkenazi Jewish in 37 of 9860 chromosomes (freq: 0.003753) and African in 55 of 23612 chromosomes (freq: 0.002329), but was not observed in the East Asian population. The p.Ile208 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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