ClinVar Miner

Submissions for variant NM_005921.2(MAP3K1):c.3084A>G (p.Gln1028=)

gnomAD frequency: 0.07871  dbSNP: rs3822625
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001522463 SCV001732016 benign 46,XY sex reversal 6 2024-01-29 criteria provided, single submitter clinical testing
GeneDx RCV001685417 SCV001903049 benign not provided 2018-11-12 criteria provided, single submitter clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV001522463 SCV002557318 benign 46,XY sex reversal 6 2022-06-24 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Benign. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with 46XY sex reversal 6 (MIM#613762) (PMIDs: 24135036, 21129722, 30608580). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Intrafamilial and interfamilial variability have been reported, ranging from hypospadias to complete gonadal dysgenesis (PMIDs: 27899157, 12476449, 21129722). (I) 0212 - Non-canonical splice site variant without proven consequence on splicing (no functional evidence available). (I) 0251 - This variant is heterozygous. (I) 0308 - Population frequency for this variant is out of keeping with known incidence of 46XY sex reversal 6 (MIM#613762) (gnomAD v2: 18666 heterozygotes, 807 homozygotes). (SB) 0508 - In silico predictions for abnormal splicing are conflicting. (I) 0604 - Variant is not located in an established domain, motif, hotspot or informative constraint region. (I) 0705 - No comparable single nucleotide substitution variants have previous evidence for pathogenicity. (I) 0806 - This variant has moderate previous evidence of being benign in unrelated individuals. It has been reported as benign by clinical testing laboratories (ClinVar). It has also been reported in one unrelated patient with 46,XY disorder of sex development, however there was no convincing evidence for its pathogenicity (PMIDs: 24497709, 28504475). (SB) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Breakthrough Genomics, Breakthrough Genomics RCV001685417 SCV005301131 benign not provided criteria provided, single submitter not provided

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