ClinVar Miner

Submissions for variant NM_001754.4(RUNX1):c.1389C>G (p.Pro463=) (rs61750222)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Myeloid Malignancy Variant Curation Expert Panel RCV000327560 SCV000965632 benign Familial platelet disorder with associated myeloid malignancy 2019-08-02 reviewed by expert panel curation The MAF for the synonymous variant, NM_001754.4:c.1389C>G (p.Pro463=) is 0.1206 (12%, 1976/16382 alleles) in the African subpopulation of the gnomAD cohort, which is >/= 0.0015 (0.15%) (BA1). This variant is predicted by SSF and MES to lead to an increase in the canonical splice site score or a decrease of the canonical splice site score by no more than 10% AND no putative cryptic splice sites are created (BP4). This synonymous variant is predicted by evolutionary conservation prediction algorithms that the site is not conserved (PhyloP score -0.503315 <0.1) (BP7). This variant is detected in a homozygous state in 202 individuals in a gnomAD (BP2). In summary, this variant meets criteria to be classified as benign. ACMG/AMP criteria applied, as specified by the Myeloid Malignancy Variant Curation Expert Panel for RUNX1: BA1, BP2, BP4, BP7.
PreventionGenetics,PreventionGenetics RCV000241802 SCV000308030 benign not specified 2018-04-03 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000327560 SCV000435942 benign Familial platelet disorder with associated myeloid malignancy 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.

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