rs3176894

Positions:

• chr10-95754702-G-A
• chr10-95754702-G-C

Variant summary

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

The NM_001098175.2(ENTPD1):​c.37+42709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,218 control chromosomes in the GnomAD database, including 52,954 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 0.83 (52952 hom., cov: 33)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: ENTPD1 NM_001098175.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD1	NM_001098175.2	c.37+42709G>A		intron_variant			NP_001091645.1
ENTPD1	XM_011540371.3	c.37+42709G>A		intron_variant			XP_011538673.1
ENTPD1	XM_047426023.1	c.37+42709G>A		intron_variant			XP_047281979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000453258.6	c.37+42709G>A		intron_variant		1		ENSP00000390955.2
ENTPD1-AS1	ENST00000416301.5	n.2745C>T		non_coding_transcript_exon_variant	6/6	2
ENTPD1-AS1	ENST00000669711.1	n.1351+660C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126126 AN: 152096 Hom.: 52924 Cov.: 33

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.832

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

Gnomad4 FIN exome AF: 1.00

GnomAD4 genome AF: 0.829 AC: 126203 AN: 152214 Hom.: 52952 Cov.: 33 AF XY: 0.826 AC XY: 61492 AN XY: 74410

Gnomad4 AFR AF: 0.920

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.777

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.810

Gnomad4 OTH AF: 0.827

Alfa AF: 0.772 Hom.: 2297

Bravo AF: 0.838

Asia WGS AF: 0.633 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3176894; hg19: chr10-97514459;