Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_StrongBA1
The NM_024006(VKORC1):c.*134G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 151832 control chromosomes in the gnomAD Genomes database, including 12858 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★).
Verdict is Benign. Variant got -16 ACMG points.
GnomAD3 genomes AF: 0.403AC: 61172AN: 151832Hom.: 12858Cov.: 31 GnomAD4 exome AF: 0.390AC: 496903AN: 1274084Hom.: 102978 AF XY: 0.397AC XY: 250851AN XY: 631166
Submissions by phenotype
Vitamin K-dependent clotting factors, combined deficiency of, type 2
|Benign, criteria provided, single submitter||clinical testing||Illumina Laboratory Services, Illumina||Jan 12, 2018||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. -|
warfarin response - Dosage
|drug response, reviewed by expert panel||curation||PharmGKB||Mar 24, 2021||PharmGKB Level of Evidence 1B: Level 1B clinical annotations describe variant-drug combinations with a high level of evidence supporting the association but no variant-specific prescribing guidance in an annotated clinical guideline or FDA drug label. Level 1B clinical annotations must be supported by at least two independent publications. Drug-variant association: Dosage|
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