ClinVar Miner

Submissions for variant NM_000133.4(F9):c.580A>G (p.Thr194Ala)

gnomAD frequency: 0.22614  dbSNP: rs6048
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Coagulation Factor Deficiency Variant Curation Expert Panel, Clingen RCV000396693 SCV004363688 benign Hereditary factor IX deficiency disease 2024-02-09 reviewed by expert panel curation The c.580A>G (p.Thr194Ala) variant is reported at an MAF of 0.3026 (27985/92495 alleles) in the non-Finnish European population in gnomAD v2.1.1 with 2609 homozygotes and 10667 hemizygotes, meeting BA1 criteria of MAF > 0.0000556. Note that gnomAD v3.1.1 reports a frequency of 0.3041 in the NFE population, with 1859 homozygotes and 4024 hemizygotes. This missense variant has a REVEL score of 0.255 (<0.3) and SpliceAI predicts no impact on splicing, with a score of 0.0, meeting BP4 criteria. In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Coagulation Factor Deficiency Variant Curation Expert Panel for F9: BA1, BP4.
PreventionGenetics, part of Exact Sciences RCV000244191 SCV000302448 benign not specified criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000244191 SCV000339741 benign not specified 2016-02-12 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000396693 SCV000481883 benign Hereditary factor IX deficiency disease 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001810847 SCV000603534 benign not provided 2021-11-25 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001521358 SCV001730689 benign Hereditary factor IX deficiency disease; Thrombophilia, X-linked, due to factor 9 defect 2024-02-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000396693 SCV001933896 benign Hereditary factor IX deficiency disease 2021-08-10 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001701639 SCV001933907 benign Thrombophilia, X-linked, due to factor 9 defect 2021-08-10 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV001810847 SCV005279616 benign not provided criteria provided, single submitter not provided
OMIM RCV000011334 SCV000031565 protective Deep venous thrombosis, protection against 2009-05-01 no assertion criteria provided literature only
Natera, Inc. RCV000396693 SCV001458781 benign Hereditary factor IX deficiency disease 2020-09-16 no assertion criteria provided clinical testing

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