10-95869237-A-G

Variant names:

• chr10-95869237-A-G
• rs2226163
• NM_001776.6:c.*2854A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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]

ENSG00000270099 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001776.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	NM_001776.6	MANE Select	c.*2854A>G		3_prime_UTR	Exon 10 of 10	NP_001767.3
	ENTPD1	NM_001440932.1		c.*2854A>G		3_prime_UTR	Exon 10 of 10	NP_001427861.1
	ENTPD1	NM_001164178.1		c.*2854A>G		3_prime_UTR	Exon 10 of 10	NP_001157650.1	P49961-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000371205.5	TSL:1 MANE Select	c.*2854A>G		3_prime_UTR	Exon 10 of 10	ENSP00000360248.4	P49961-1
	ENTPD1	ENST00000453258.6	TSL:1	c.*2854A>G		3_prime_UTR	Exon 10 of 10	ENSP00000390955.2	P49961-2
	ENSG00000270099	ENST00000491114.1	TSL:5	n.171+4376A>G		intron	N/A	ENSP00000473305.1	R4GMQ9

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

African (AFR) AF: 0.504 AC: 6514 AN: 12932

American (AMR) AF: 0.685 AC: 596 AN: 870

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1918 AN: 4022

East Asian (EAS) AF: 0.325 AC: 794 AN: 2442

South Asian (SAS) AF: 0.610 AC: 8381 AN: 13738

European-Finnish (FIN) AF: 0.578 AC: 126 AN: 218

Middle Eastern (MID) AF: 0.479 AC: 595 AN: 1242

European-Non Finnish (NFE) AF: 0.598 AC: 385181 AN: 643730

Other (OTH) AF: 0.573 AC: 12889 AN: 22490

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

African (AFR) AF: 0.456 AC: 15450 AN: 33884

American (AMR) AF: 0.608 AC: 7605 AN: 12516

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1206 AN: 3278

East Asian (EAS) AF: 0.248 AC: 1092 AN: 4406

South Asian (SAS) AF: 0.546 AC: 2252 AN: 4128

European-Finnish (FIN) AF: 0.506 AC: 3047 AN: 6020

Middle Eastern (MID) AF: 0.375 AC: 87 AN: 232

European-Non Finnish (NFE) AF: 0.525 AC: 33215 AN: 63288

Other (OTH) AF: 0.470 AC: 851 AN: 1812

Alfa AF: 0.468 Hom.: 3374

Bravo AF: 0.511

Asia WGS AF: 0.370 AC: 1145 AN: 3086

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.33
DANN	Benign	0.45
PhyloP100		-0.70
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2226163;

hg19: chr10-97628994;