rs3181121

chr10-95858823-T-C

Variant summary

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

The NM_001776.6(ENTPD1):c.1075-1646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0731 in 152,128 control chromosomes in the GnomAD database, including 448 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 0.073 (448 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001776.6	c.1075-1646T>C		intron_variant		ENST00000371205.5
ENTPD1-AS1	NR_038444.1	n.440-11338A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000371205.5	c.1075-1646T>C		intron_variant		1	NM_001776.6	P1
	ENST00000433113.1	n.261-14609T>C		intron_variant, non_coding_transcript_variant		2
ENTPD1-AS1	ENST00000669711.1	n.443+17695A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11115 AN: 152010 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0905

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0731 AC: 11123 AN: 152128 Hom.: 448 Cov.: 32 AF XY: 0.0730 AC XY: 5434 AN XY: 74388

Gnomad4 AFR AF: 0.0949

Gnomad4 AMR AF: 0.0631

Gnomad4 ASJ AF: 0.0280

Gnomad4 EAS AF: 0.0471

Gnomad4 SAS AF: 0.0899

Gnomad4 FIN AF: 0.0730

Gnomad4 NFE AF: 0.0646

Gnomad4 OTH AF: 0.0643

Alfa AF: 0.0632 Hom.: 439

Bravo AF: 0.0721

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.4
Dann	Benign	0.56

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: rs3181121; hg19: chr10-97618580;