16-31093188-C-G
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_StrongBA1
The NM_024006.6(VKORC1):c.283+124G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,025,128 control chromosomes in the GnomAD database, including 86,595 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★).
Frequency
Consequence
NM_024006.6 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VKORC1 | NM_024006.6 | c.283+124G>C | intron_variant | Intron 2 of 2 | ENST00000394975.3 | NP_076869.1 | ||
VKORC1 | NM_001311311.2 | c.283+124G>C | intron_variant | Intron 2 of 3 | NP_001298240.1 | |||
VKORC1 | NM_206824.3 | c.173+1369G>C | intron_variant | Intron 1 of 1 | NP_996560.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.377 AC: 55851AN: 148126Hom.: 11456 Cov.: 28
GnomAD4 exome AF: 0.394 AC: 345271AN: 876912Hom.: 75139 AF XY: 0.386 AC XY: 172679AN XY: 446832
GnomAD4 genome AF: 0.377 AC: 55856AN: 148216Hom.: 11456 Cov.: 28 AF XY: 0.378 AC XY: 27288AN XY: 72154
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
warfarin response - Dosage Other:1
PharmGKB Level of Evidence 2A: Variants in Level 2A clinical annotations are found in PharmGKB’s Tier 1 Very Important Pharmacogenes (VIPs). These variants are in known pharmacogenes, implying causation of drug phenotype is more likely. These clinical annotations describe variant-drug combinations with a moderate level of evidence supporting the association. For example, the association may be found in multiple cohorts, but there may be a minority of studies that do not support the majority assertion. Level 2A clinical annotations must be supported by at least two independent publications. Drug-variant association: Dosage
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at