rs7294
Variant summary
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 (β β β ).
Frequency
Genomes: π 0.40 ( 12858 hom., cov: 31)
Consequence
VKORC1
NM_024006 3_prime_UTR
NM_024006 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.00200
Links
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BP6
?
Variant 16:31091000-C>T is Benign according to our data. Variant chr16-31091000-C-T is described in ClinVar as [drug_response]. Clinvar id is 226016. Status of the report is reviewed_by_expert_panel, 3 stars. We mark this variant Likely_benign, oryginal submissions are: {Benign=1, drug_response=1}.
BA1
?
GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VKORC1 | NM_024006.6 | c.*134G>A | 3_prime_UTR_variant | 3/3 | ENST00000394975.3 | ||
VKORC1 | NM_001311311.2 | c.*134G>A | 3_prime_UTR_variant | 4/4 | |||
VKORC1 | NM_206824.3 | c.*237G>A | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VKORC1 | ENST00000394975.3 | c.*134G>A | 3_prime_UTR_variant | 3/3 | 1 | NM_024006.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.403 AC: 61172AN: 151832Hom.: 12858 Cov.: 31
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GnomAD4 exome AF: 0.390 AC: 496903AN: 1274084Hom.: 102978 AF XY: 0.397 AC XY: 250851AN XY: 631166
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ClinVar
Significance: drug response
Submissions summary: Benign:1Other:1
Revision: reviewed by expert panel
LINK: link
Submissions by phenotype
Vitamin K-dependent clotting factors, combined deficiency of, type 2 Benign:1
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 Other:1
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 |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
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RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out SpliceAI and Pangolin per-transcript scores at