rs3181118

Variant names:

• chr10-95863619-C-T
• rs3181118
• NM_001776.6:c.1189-1105C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001776.6(ENTPD1):​c.1189-1105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,246 control chromosomes in the GnomAD database, including 129 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 0.037 (129 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97
• Publications: 7 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]

ENSG00000270099 (HGNC:):

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=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0371 (5652/152246) while in subpopulation NFE AF = 0.0494 (3359/68016). AF 95% confidence interval is 0.048. There are 129 homozygotes in GnomAd4. There are 2738 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 129 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.1189-1105C>T		intron_variant	Intron 8 of 9	ENST00000371205.5	NP_001767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5	c.1189-1105C>T		intron_variant	Intron 8 of 9	1	NM_001776.6	ENSP00000360248.4
ENSG00000270099	ENST00000491114.1	n.34-1105C>T		intron_variant	Intron 1 of 6	5		ENSP00000473305.1

Frequencies

GnomAD3 genomes AF: 0.0372 AC: 5654 AN: 152128 Hom.: 129 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0371 AC: 5652 AN: 152246 Hom.: 129 Cov.: 32 AF XY: 0.0368 AC XY: 2738 AN XY: 74448

African (AFR) AF: 0.0264 AC: 1096 AN: 41532

American (AMR) AF: 0.0287 AC: 439 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0550 AC: 191 AN: 3472

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0102 AC: 49 AN: 4822

European-Finnish (FIN) AF: 0.0382 AC: 405 AN: 10598

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0494 AC: 3359 AN: 68016

Other (OTH) AF: 0.0379 AC: 80 AN: 2112

Alfa AF: 0.0445 Hom.: 276

Bravo AF: 0.0356

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.25
DANN	Benign	0.63
PhyloP100		-2.0
Mutation Taster		=100/0	polymorphism

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: rs3181118; hg19: chr10-97623376;