10-95832399-A-T

Variant names:

• chr10-95832399-A-T
• rs12763743
• NM_001776.6:c.145-7292A>T

Variant summary

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

The NM_001776.6(ENTPD1):​c.145-7292A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,144 control chromosomes in the GnomAD database, including 1,156 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1156 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.157
• Publications: 4 publications found

Genes affected

ENTPD1 (HGNC:3363): (ectonucleoside triphosphate diphosphohydrolase 1) The protein encoded by this gene is a plasma membrane protein that hydrolyzes extracellular ATP and ADP to AMP. Inhibition of this protein's activity may confer anticancer benefits. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2015]

ENTPD1-AS1 (HGNC:45203): (ENTPD1 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.145-7292A>T		intron_variant	Intron 2 of 9	ENST00000371205.5	NP_001767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5	c.145-7292A>T		intron_variant	Intron 2 of 9	1	NM_001776.6	ENSP00000360248.4

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17846 AN: 152026 Hom.: 1151 Cov.: 32

Gnomad AFR AF: 0.0859

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.0408

Gnomad SAS AF: 0.0735

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.117 AC: 17858 AN: 152144 Hom.: 1156 Cov.: 32 AF XY: 0.117 AC XY: 8704 AN XY: 74378

African (AFR) AF: 0.0861 AC: 3574 AN: 41512

American (AMR) AF: 0.104 AC: 1586 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 723 AN: 3470

East Asian (EAS) AF: 0.0411 AC: 213 AN: 5182

South Asian (SAS) AF: 0.0736 AC: 355 AN: 4826

European-Finnish (FIN) AF: 0.158 AC: 1665 AN: 10570

Middle Eastern (MID) AF: 0.219 AC: 64 AN: 292

European-Non Finnish (NFE) AF: 0.137 AC: 9287 AN: 68000

Other (OTH) AF: 0.141 AC: 296 AN: 2106

Alfa AF: 0.123 Hom.: 176

Bravo AF: 0.113

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.2
DANN	Benign	0.67
PhyloP100		-0.16
Mutation Taster		=100/0	polymorphism (auto)

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: rs12763743; hg19: chr10-97592156;