chr10-95869237-A-G

Position:

• chr10-95869237-A-G

Variant summary

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

The NM_001776.6(ENTPD1):​c.*2854A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 130,414 control chromosomes in the GnomAD database, including 16,012 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 0.50 (16012 hom., cov: 21)
  • Exomes 𝑓: 0.59 (112073 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENTPD1 NM_001776.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001776.6	c.*2854A>G		3_prime_UTR_variant	10/10	ENST00000371205.5
ENTPD1-AS1	NR_038444.1	n.439+7281T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000371205.5	c.*2854A>G		3_prime_UTR_variant	10/10	1	NM_001776.6	P1
	ENST00000433113.1	n.261-4195A>G		intron_variant, non_coding_transcript_variant		2
ENTPD1-AS1	ENST00000669711.1	n.443+7281T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.501 AC: 65294 AN: 130402 Hom.: 16010 Cov.: 21

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.598

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.248

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.506

Gnomad MID AF: 0.378

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.472

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.594 AC: 416994 AN: 701684 Hom.: 112073 Cov.: 8 AF XY: 0.594 AC XY: 193256 AN XY: 325232

Gnomad4 AFR exome AF: 0.504

Gnomad4 AMR exome AF: 0.685

Gnomad4 ASJ exome AF: 0.477

Gnomad4 EAS exome AF: 0.325

Gnomad4 SAS exome AF: 0.610

Gnomad4 FIN exome AF: 0.578

Gnomad4 NFE exome AF: 0.598

Gnomad4 OTH exome AF: 0.573

GnomAD4 genome AF: 0.501 AC: 65313 AN: 130414 Hom.: 16012 Cov.: 21 AF XY: 0.502 AC XY: 31105 AN XY: 61926

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.368

Gnomad4 EAS AF: 0.248

Gnomad4 SAS AF: 0.546

Gnomad4 FIN AF: 0.506

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.470

Alfa AF: 0.459 Hom.: 2751

Bravo AF: 0.511

Asia WGS AF: 0.370 AC: 1145 AN: 3086

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.45

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: rs2226163; hg19: chr10-97628994;