rs3949478

Positions:

• chr10-95713457-A-G
• chr10-95713457-A-T

Variant summary

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

The ENST00000453258.6(ENTPD1):​c.37+1464A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,132 control chromosomes in the GnomAD database, including 41,168 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 0.73 (41168 hom., cov: 33)
• Consequence: ENTPD1 ENST00000453258.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.792 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD1	NM_001098175.2	c.37+1464A>G		intron_variant			NP_001091645.1
ENTPD1	XM_011540371.3	c.37+1464A>G		intron_variant			XP_011538673.1
ENTPD1	XM_047426023.1	c.37+1464A>G		intron_variant			XP_047281979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000453258.6	c.37+1464A>G		intron_variant		1		ENSP00000390955

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110994 AN: 152014 Hom.: 41163 Cov.: 33

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.777

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.828

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.754

Gnomad MID AF: 0.829

Gnomad NFE AF: 0.797

Gnomad OTH AF: 0.744

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

GnomAD4 genome AF: 0.730 AC: 111042 AN: 152132 Hom.: 41168 Cov.: 33 AF XY: 0.727 AC XY: 54051 AN XY: 74378

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.828

Gnomad4 EAS AF: 0.780

Gnomad4 SAS AF: 0.656

Gnomad4 FIN AF: 0.754

Gnomad4 NFE AF: 0.797

Gnomad4 OTH AF: 0.744

Alfa AF: 0.785 Hom.: 60475

Bravo AF: 0.729

Asia WGS AF: 0.693 AC: 2410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.97

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3949478; hg19: chr10-97473214;