10-95791971-C-A

Variant names:

• chr10-95791971-C-A
• rs10882665
• NM_001776.6:c.17-31266C>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.17-31266C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 151,840 control chromosomes in the GnomAD database, including 4,875 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 0.23 (4875 hom., cov: 31)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.194
• 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)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.17-31266C>A		intron_variant	Intron 1 of 9	ENST00000371205.5	NP_001767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5	c.17-31266C>A		intron_variant	Intron 1 of 9	1	NM_001776.6	ENSP00000360248.4

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35253 AN: 151722 Hom.: 4862 Cov.: 31

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.217

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

GnomAD4 genome AF: 0.233 AC: 35325 AN: 151840 Hom.: 4875 Cov.: 31 AF XY: 0.236 AC XY: 17545 AN XY: 74202

African (AFR) AF: 0.378 AC: 15635 AN: 41362

American (AMR) AF: 0.214 AC: 3265 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 406 AN: 3464

East Asian (EAS) AF: 0.219 AC: 1129 AN: 5154

South Asian (SAS) AF: 0.334 AC: 1606 AN: 4802

European-Finnish (FIN) AF: 0.209 AC: 2198 AN: 10512

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

European-Non Finnish (NFE) AF: 0.153 AC: 10402 AN: 67964

Other (OTH) AF: 0.218 AC: 460 AN: 2110

Alfa AF: 0.181 Hom.: 1585

Bravo AF: 0.235

Asia WGS AF: 0.301 AC: 1045 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.1
DANN	Benign	0.61
PhyloP100		-0.19
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: rs10882665; hg19: chr10-97551728;