rs1342790

chr10-95840782-G-Achr10-95840782-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001776.6(ENTPD1):c.262+974G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 151,970 control chromosomes in the GnomAD database, including 22,162 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 0.53 (22162 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.180

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001776.6	c.262+974G>A		intron_variant		ENST00000371205.5
ENTPD1-AS1	NR_038444.1	n.533+6610C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000371205.5	c.262+974G>A		intron_variant		1	NM_001776.6	P1
	ENST00000433113.1	n.260+7015G>A		intron_variant, non_coding_transcript_variant		2
ENTPD1-AS1	ENST00000669711.1	n.443+35736C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.535 AC: 81173 AN: 151852 Hom.: 22139 Cov.: 32

Gnomad AFR AF: 0.527

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.628

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.261

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.502

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

GnomAD4 genome AF: 0.535 AC: 81246 AN: 151970 Hom.: 22162 Cov.: 32 AF XY: 0.537 AC XY: 39900 AN XY: 74268

Gnomad4 AFR AF: 0.527

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.558

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.499

Alfa AF: 0.539 Hom.: 2704

Bravo AF: 0.538

Asia WGS AF: 0.439 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.3
Dann	Benign	0.43

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: rs1342790; hg19: chr10-97600539;