16-31096368-C-T

Variant names:

• chr16-31096368-C-T
• rs9923231

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.319 in 152,092 control chromosomes in the GnomAD database, including 10,015 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★).

• Frequency: Genomes: 𝑓 0.32 (10015 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: drug response reviewed by expert panel P:1 U:2 B:4 O:8
• Conservation: PhyloP100: -0.417
• Publications: 886 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48521 AN: 151974 Hom.: 10014 Cov.: 32

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.499

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.378

Gnomad OTH AF: 0.391

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.319 AC: 48520 AN: 152092 Hom.: 10015 Cov.: 32 AF XY: 0.322 AC XY: 23921 AN XY: 74344

African (AFR) AF: 0.0998 AC: 4141 AN: 41504

American (AMR) AF: 0.391 AC: 5974 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.499 AC: 1734 AN: 3472

East Asian (EAS) AF: 0.892 AC: 4612 AN: 5172

South Asian (SAS) AF: 0.178 AC: 859 AN: 4824

European-Finnish (FIN) AF: 0.391 AC: 4127 AN: 10558

Middle Eastern (MID) AF: 0.534 AC: 156 AN: 292

European-Non Finnish (NFE) AF: 0.378 AC: 25693 AN: 67986

Other (OTH) AF: 0.389 AC: 824 AN: 2116

Alfa AF: 0.371 Hom.: 23218

Bravo AF: 0.323

Asia WGS AF: 0.460 AC: 1603 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: drug response

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (2)
-	-	1	not specified (1)
-	1	-	See cases (1)
-	1	-	Thrombus (1)
-	-	1	VKORC1-related disorder (1)
1	-	-	Warfarin response (2)
-	-	-	acenocoumarol response - Dosage (1)
-	-	-	phenprocoumon response - Dosage (1)
-	-	-	phenprocoumon response - Toxicity (1)
-	-	-	Venous thromboembolism (1)
-	-	-	warfarin response - Dosage (1)
-	-	-	warfarin response - Efficacy (1)
-	-	-	warfarin response - Toxicity (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.5
DANN	Benign	0.33
PhyloP100		-0.42
PromoterAI		0.013	Neutral

Splicing

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

Other links and lift over

dbSNP: rs9923231; hg19: chr16-31107689;