16-31093188-C-G

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_Strong BP6_Strong BA1

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:
  • Genomes: 𝑓 0.38 (11456 hom., cov: 28)
  • Exomes 𝑓: 0.39 (75139 hom.)
• Consequence: VKORC1 NM_024006.6 intron
• Clinical Significance: drug response reviewed by expert panel B:1 O:1
• Conservation: PhyloP100: -0.576

Genes affected

VKORC1 (HGNC:23663): (vitamin K epoxide reductase complex subunit 1) This gene encodes the catalytic subunit of the vitamin K epoxide reductase complex, which is responsible for the reduction of inactive vitamin K 2,3-epoxide to active vitamin K in the endoplasmic reticulum membrane. Vitamin K is a required co-factor for carboxylation of glutamic acid residues by vitamin K-dependent gamma-carboxylase in blood-clotting enzymes. Allelic variation in this gene is associated with vitamin k-dependent clotting factors combined deficiency of 2, and increased resistance or sensitivity to warfarin, an inhibitor of vitamin K epoxide reductase. Pseudogenes of this gene are located on chromosomes 1 and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]

ACMG classification

Verdict is Benign. Variant got -16 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 16-31093188-C-G is Benign according to our data. Variant chr16-31093188-C-G is described in ClinVar as [drug_response]. Clinvar id is 226026.Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_benign, oryginal submissions are: {drug_response=1, Likely_benign=1}.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
VKORC1	NM_024006.6	c.283+124G>C		intron_variant		ENST00000394975.3
VKORC1	NM_001311311.2	c.283+124G>C		intron_variant
VKORC1	NM_206824.3	c.173+1369G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
VKORC1	ENST00000394975.3	c.283+124G>C		intron_variant		1	NM_024006.6	P1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 55851 AN: 148126 Hom.: 11456 Cov.: 28

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.498

Gnomad EAS AF: 0.894

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.556

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.438

GnomAD4 exome AF: 0.394 AC: 345271 AN: 876912 Hom.: 75139 AF XY: 0.386 AC XY: 172679 AN XY: 446832

Gnomad4 AFR exome AF: 0.261

Gnomad4 AMR exome AF: 0.463

Gnomad4 ASJ exome AF: 0.485

Gnomad4 EAS exome AF: 0.905

Gnomad4 SAS exome AF: 0.193

Gnomad4 FIN exome AF: 0.391

Gnomad4 NFE exome AF: 0.383

Gnomad4 OTH exome AF: 0.408

GnomAD4 genome AF: 0.377 AC: 55856 AN: 148216 Hom.: 11456 Cov.: 28 AF XY: 0.378 AC XY: 27288 AN XY: 72154

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.498

Gnomad4 EAS AF: 0.894

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.437

Alfa AF: 0.383 Hom.: 6711

Bravo AF: 0.381

Asia WGS AF: 0.470 AC: 1638 AN: 3478

ClinVar

Significance: drug response

Submissions summary: Benign:1 Other:1

Revision: reviewed by expert panel

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 09, 2018

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

drug response, reviewed by expert panel

curation

PharmGKB

Mar 24, 2021

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: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.72
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8050894; hg19: chr16-31104509;