10-95840782-G-A

Variant names:

• chr10-95840782-G-A
• rs1342790
• NM_001776.6:c.262+974G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001776.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	NM_001776.6	MANE Select	c.262+974G>A		intron	N/A	NP_001767.3
	ENTPD1	NM_001440932.1		c.340+974G>A		intron	N/A	NP_001427861.1
	ENTPD1	NM_001164178.1		c.298+974G>A		intron	N/A	NP_001157650.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000371205.5	TSL:1 MANE Select	c.262+974G>A		intron	N/A	ENSP00000360248.4
	ENTPD1	ENST00000453258.6	TSL:1	c.283+974G>A		intron	N/A	ENSP00000390955.2
	ENTPD1	ENST00000635076.1	TSL:1	n.145-3694G>A		intron	N/A	ENSP00000489250.1

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

African (AFR) AF: 0.527 AC: 21834 AN: 41438

American (AMR) AF: 0.628 AC: 9591 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1338 AN: 3466

East Asian (EAS) AF: 0.262 AC: 1351 AN: 5166

South Asian (SAS) AF: 0.563 AC: 2712 AN: 4818

European-Finnish (FIN) AF: 0.558 AC: 5881 AN: 10538

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36809 AN: 67964

Other (OTH) AF: 0.499 AC: 1054 AN: 2112

Alfa AF: 0.539 Hom.: 2821

Bravo AF: 0.538

Asia WGS AF: 0.439 AC: 1528 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		0.18
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: rs1342790; hg19: chr10-97600539;