rs3181118

Positions:

• chr10-95863619-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001776.6(ENTPD1):​c.1189-1105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0371 in 152,246 control chromosomes in the GnomAD database, including 129 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 0.037 (129 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

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]

(HGNC:):

ENTPD1-AS1 (HGNC:45203): (ENTPD1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0371 (5652/152246) while in subpopulation NFE AF= 0.0494 (3359/68016). AF 95% confidence interval is 0.048. There are 129 homozygotes in gnomad4. There are 2738 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 129 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001776.6	c.1189-1105C>T		intron_variant		ENST00000371205.5
ENTPD1-AS1	NR_038444.1	n.439+12899G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000371205.5	c.1189-1105C>T		intron_variant		1	NM_001776.6	P1
	ENST00000433113.1	n.261-9813C>T		intron_variant, non_coding_transcript_variant		2
ENTPD1-AS1	ENST00000669711.1	n.443+12899G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0372 AC: 5654 AN: 152128 Hom.: 129 Cov.: 32

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.0230

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.0550

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0106

Gnomad FIN AF: 0.0382

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0383

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

GnomAD4 genome AF: 0.0371 AC: 5652 AN: 152246 Hom.: 129 Cov.: 32 AF XY: 0.0368 AC XY: 2738 AN XY: 74448

Gnomad4 AFR AF: 0.0264

Gnomad4 AMR AF: 0.0287

Gnomad4 ASJ AF: 0.0550

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0102

Gnomad4 FIN AF: 0.0382

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0379

Alfa AF: 0.0454 Hom.: 229

Bravo AF: 0.0356

Asia WGS AF: 0.00664 AC: 23 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.25
DANN	Benign	0.63

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181118; hg19: chr10-97623376;