10-94761900-C-T

Variant names:

• chr10-94761900-C-T
• rs12248560
• ENST00000464755.1:n.932-13158C>T

Variant summary

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

The ENST00000464755.1(ENSG00000276490):​n.932-13158C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 151,940 control chromosomes in the GnomAD database, including 3,261 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as drug response (★★★★).

• Frequency: Genomes: 𝑓 0.20 (3261 hom., cov: 32)
• Consequence: ENSG00000276490 ENST00000464755.1 intron
• Clinical Significance: drug response practice guideline B:1 O:3
• Conservation: PhyloP100: -0.799
• Publications: 551 publications found

Genes affected

ENSG00000276490 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000464755.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000276490	ENST00000464755.1	TSL:2	n.932-13158C>T		intron	N/A	ENSP00000483243.1

Frequencies

GnomAD3 genomes AF: 0.200 AC: 30383 AN: 151824 Hom.: 3260 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.213

Gnomad EAS AF: 0.00945

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.200 AC: 30385 AN: 151940 Hom.: 3261 Cov.: 32 AF XY: 0.197 AC XY: 14601 AN XY: 74238

African (AFR) AF: 0.221 AC: 9161 AN: 41430

American (AMR) AF: 0.133 AC: 2031 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.213 AC: 740 AN: 3468

East Asian (EAS) AF: 0.00947 AC: 49 AN: 5174

South Asian (SAS) AF: 0.163 AC: 785 AN: 4820

European-Finnish (FIN) AF: 0.185 AC: 1943 AN: 10506

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14949 AN: 67948

Other (OTH) AF: 0.198 AC: 418 AN: 2112

Alfa AF: 0.212 Hom.: 1020

Bravo AF: 0.196

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

ClinVar submissions as Germline

Significance: drug response

Revision: practice guideline

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (2)
-	-	-	Clopidogrel response (1)
-	-	-	CYP2C19: increased function (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.27
DANN	Benign	0.50
PhyloP100		-0.80

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

Other links and lift over

dbSNP: rs12248560; hg19: chr10-96521657;