rs10748643

Variant names:

• chr10-95757007-A-G
• rs10748643
• NM_001776.6:c.16+752A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001776.6(ENTPD1):​c.16+752A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,020 control chromosomes in the GnomAD database, including 22,553 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 0.54 (22553 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.965
• Publications: 24 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.16+752A>G		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.16+752A>G		intron_variant	Intron 1 of 9	1	NM_001776.6	ENSP00000360248.4

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81937 AN: 151902 Hom.: 22537 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.539 AC: 82000 AN: 152020 Hom.: 22553 Cov.: 32 AF XY: 0.542 AC XY: 40239 AN XY: 74302

African (AFR) AF: 0.545 AC: 22604 AN: 41460

American (AMR) AF: 0.626 AC: 9569 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3468

East Asian (EAS) AF: 0.262 AC: 1353 AN: 5172

South Asian (SAS) AF: 0.563 AC: 2716 AN: 4824

European-Finnish (FIN) AF: 0.557 AC: 5886 AN: 10566

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36801 AN: 67938

Other (OTH) AF: 0.500 AC: 1055 AN: 2108

Alfa AF: 0.558 Hom.: 10558

Bravo AF: 0.543

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	-0.45
CADD	Benign	17
DANN	Benign	0.74
PhyloP100		0.96
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs10748643; hg19: chr10-97516764;