rs3181123

Variant names:

• chr10-95847318-C-T
• rs3181123
• NM_001776.6:c.814-128C>T

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001776.6(ENTPD1):​c.814-128C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,081,116 control chromosomes in the GnomAD database, including 22,517 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.23 (4591 hom., cov: 32)
  • Exomes 𝑓: 0.19 (17926 hom.)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.741
• Publications: 5 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)

ENSG00000240527 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 10-95847318-C-T is Benign according to our data. Variant chr10-95847318-C-T is described in ClinVar as Benign. ClinVar VariationId is 1293400.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.355 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.814-128C>T		intron_variant	Intron 6 of 9	ENST00000371205.5	NP_001767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5	c.814-128C>T		intron_variant	Intron 6 of 9	1	NM_001776.6	ENSP00000360248.4

Frequencies

GnomAD3 genomes AF: 0.227 AC: 34554 AN: 151942 Hom.: 4578 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.186 AC: 172817 AN: 929056 Hom.: 17926 AF XY: 0.190 AC XY: 91725 AN XY: 483296

African (AFR) AF: 0.363 AC: 8632 AN: 23774

American (AMR) AF: 0.231 AC: 9645 AN: 41788

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 2667 AN: 22818

East Asian (EAS) AF: 0.264 AC: 9774 AN: 37088

South Asian (SAS) AF: 0.312 AC: 23213 AN: 74336

European-Finnish (FIN) AF: 0.192 AC: 8665 AN: 45068

Middle Eastern (MID) AF: 0.160 AC: 651 AN: 4066

European-Non Finnish (NFE) AF: 0.160 AC: 101649 AN: 637284

Other (OTH) AF: 0.185 AC: 7921 AN: 42834

GnomAD4 genome AF: 0.228 AC: 34626 AN: 152060 Hom.: 4591 Cov.: 32 AF XY: 0.232 AC XY: 17223 AN XY: 74332

African (AFR) AF: 0.360 AC: 14906 AN: 41424

American (AMR) AF: 0.215 AC: 3285 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 405 AN: 3468

East Asian (EAS) AF: 0.220 AC: 1140 AN: 5182

South Asian (SAS) AF: 0.333 AC: 1603 AN: 4816

European-Finnish (FIN) AF: 0.208 AC: 2198 AN: 10580

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10411 AN: 67986

Other (OTH) AF: 0.215 AC: 454 AN: 2110

Alfa AF: 0.176 Hom.: 1692

Bravo AF: 0.230

Asia WGS AF: 0.299 AC: 1041 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Nov 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.4
DANN	Benign	0.66
PhyloP100		-0.74
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: rs3181123; hg19: chr10-97607075;