rs1933166

Positions:

• chr10-95727605-A-G

Variant summary

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

The ENST00000453258.6(ENTPD1):​c.37+15612A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,118 control chromosomes in the GnomAD database, including 2,494 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 0.16 (2494 hom., cov: 32)
• Consequence: ENTPD1 ENST00000453258.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.350

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD1	NM_001098175.2	c.37+15612A>G		intron_variant			NP_001091645.1
ENTPD1	XM_011540371.3	c.37+15612A>G		intron_variant			XP_011538673.1
ENTPD1	XM_047426023.1	c.37+15612A>G		intron_variant			XP_047281979.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000453258.6	c.37+15612A>G		intron_variant		1		ENSP00000390955

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24174 AN: 152000 Hom.: 2486 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.0893

Gnomad EAS AF: 0.173

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.159 AC: 24233 AN: 152118 Hom.: 2494 Cov.: 32 AF XY: 0.163 AC XY: 12108 AN XY: 74374

Gnomad4 AFR AF: 0.281

Gnomad4 AMR AF: 0.150

Gnomad4 ASJ AF: 0.0893

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.0892

Gnomad4 OTH AF: 0.154

Alfa AF: 0.107 Hom.: 1344

Bravo AF: 0.163

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.3
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1933166; hg19: chr10-97487362;