rs11188513

chr10-95873264-C-T

Variant summary

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

The NM_001776.6(ENTPD1):c.*6881C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 985,100 control chromosomes in the GnomAD database, including 215,992 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 0.66 (33319 hom., cov: 31)
  • Exomes 𝑓: 0.66 (182673 hom.)
• Consequence: ENTPD1 NM_001776.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001776.6	c.*6881C>T		3_prime_UTR_variant	10/10	ENST00000371205.5
ENTPD1-AS1	NR_038444.1	n.439+3254G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000371205.5	c.*6881C>T		3_prime_UTR_variant	10/10	1	NM_001776.6	P1
	ENST00000433113.1	n.261-168C>T		intron_variant, non_coding_transcript_variant		2
ENTPD1-AS1	ENST00000669711.1	n.443+3254G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99694 AN: 151930 Hom.: 33284 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.632

GnomAD4 exome AF: 0.661 AC: 550546 AN: 833052 Hom.: 182673 Cov.: 34 AF XY: 0.661 AC XY: 254219 AN XY: 384686

Gnomad4 AFR exome AF: 0.682

Gnomad4 AMR exome AF: 0.748

Gnomad4 ASJ exome AF: 0.569

Gnomad4 EAS exome AF: 0.247

Gnomad4 SAS exome AF: 0.624

Gnomad4 FIN exome AF: 0.663

Gnomad4 NFE exome AF: 0.665

Gnomad4 OTH exome AF: 0.633

GnomAD4 genome AF: 0.656 AC: 99785 AN: 152048 Hom.: 33319 Cov.: 31 AF XY: 0.658 AC XY: 48916 AN XY: 74336

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.559

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.659

Gnomad4 OTH AF: 0.628

Alfa AF: 0.653 Hom.: 62502

Bravo AF: 0.657

Asia WGS AF: 0.470 AC: 1637 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.14
Dann	Benign	0.53
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11188513; hg19: chr10-97633021;