rs3181123

Positions:

• chr10-95847318-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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 id 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/exons	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.814-128C>T		intron_variant		ENST00000371205.5	NP_001767.3
ENTPD1-AS1	NR_038444.1	n.533+74G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5	c.814-128C>T		intron_variant		1	NM_001776.6	ENSP00000360248	P1
	ENST00000433113.1	n.260+13551C>T		intron_variant, non_coding_transcript_variant		2
ENTPD1-AS1	ENST00000669711.1	n.443+29200G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR exome AF: 0.363

Gnomad4 AMR exome AF: 0.231

Gnomad4 ASJ exome AF: 0.117

Gnomad4 EAS exome AF: 0.264

Gnomad4 SAS exome AF: 0.312

Gnomad4 FIN exome AF: 0.192

Gnomad4 NFE exome AF: 0.160

Gnomad4 OTH exome AF: 0.185

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

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.117

Gnomad4 EAS AF: 0.220

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.215

Alfa AF: 0.176 Hom.: 1513

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.4
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181123; hg19: chr10-97607075;