16-31092854-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 2P and 9B. PM1BP4_StrongBP6BS2
The NM_001311311.2(VKORC1):c.296G>A(p.Arg99His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000936 in 1,013,254 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 5/5 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001311311.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VKORC1 | NM_024006.6 | c.283+458G>A | intron_variant | Intron 2 of 2 | ENST00000394975.3 | NP_076869.1 | ||
VKORC1 | NM_001311311.2 | c.296G>A | p.Arg99His | missense_variant | Exon 3 of 4 | NP_001298240.1 | ||
VKORC1 | NM_206824.3 | c.174-1512G>A | intron_variant | Intron 1 of 1 | NP_996560.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00108 AC: 163AN: 151596Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.00230 AC: 191AN: 82994Hom.: 2 AF XY: 0.00234 AC XY: 109AN XY: 46632
GnomAD4 exome AF: 0.000911 AC: 785AN: 861540Hom.: 6 Cov.: 12 AF XY: 0.000904 AC XY: 386AN XY: 427030
GnomAD4 genome AF: 0.00107 AC: 163AN: 151714Hom.: 1 Cov.: 31 AF XY: 0.00111 AC XY: 82AN XY: 74116
ClinVar
Submissions by phenotype
VKORC1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at