ClinVar Miner

Submissions for variant NM_000506.5(F2):c.79+7G>A

gnomAD frequency: 0.02419  dbSNP: rs3136431
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000279364 SCV000372079 likely benign Thrombophilia due to thrombin defect 2018-01-12 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Laboratory Services, Illumina RCV000956935 SCV000372080 benign Congenital prothrombin deficiency 2018-01-12 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV000956935 SCV001103727 benign Congenital prothrombin deficiency 2024-01-31 criteria provided, single submitter clinical testing
GeneDx RCV001618530 SCV001846540 benign not provided 2021-05-21 criteria provided, single submitter clinical testing
Phosphorus, Inc. RCV001823724 SCV002073402 benign not specified 2022-01-17 criteria provided, single submitter clinical testing This variant is located at 7 bp away from the canonical splice site in intron 1 out of 13 introns of the F2 gene. The variant has occurred in GnomAD with a total MAF of 0.5174% and with the highest MAF of 7.4637% in the African population. This position is not conserved. In silico splicing algorithm predicted no impact on splicing, but no functional studies were performed to confirm this prediction. This variant NM_000506.5(F2):c.79+7G>A is present in the ClinVar database (ID: 304806). Considering that the variant has a relatively high frequency in a subpopulation, it has been classified as Benign.
Breakthrough Genomics, Breakthrough Genomics RCV001618530 SCV005224269 likely benign not provided criteria provided, single submitter not provided

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