Genetic Variant ENTPD1:c.*2854A>G (chr10-95869237-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.700

Publications

9 publications found

Variant links:

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]

ENTPD1 links:

ENSG00000270099 (HGNC:):

ENSG00000270099 links:

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

ENTPD1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6 link	c.*2854A>G		3_prime_UTR_variant	Exon 10 of 10	ENST00000371205.5	NP_001767.3	P49961-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5 link	c.*2854A>G		3_prime_UTR_variant	Exon 10 of 10	1	NM_001776.6	ENSP00000360248.4		P49961-1
ENSG00000270099	ENST00000491114.1 link	n.171+4376A>G		intron_variant	Intron 2 of 6	5		ENSP00000473305.1		R4GMQ9

Frequencies

GnomAD3 genomes

AF:

0.501

AC:

65294

AN:

130402

Hom.:

16010

Cov.:

show subpopulations

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.:

AF XY:

0.594

AC XY:

193256

AN XY:

325232

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

8453

16906

25359

33812

42265

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14908

29816

44724

59632

74540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.501

AC:

65313

AN:

130414

Hom.:

16012

Cov.:

AF XY:

0.502

AC XY:

31105

AN XY:

61926

show subpopulations

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:

AN:

232

European-Non Finnish (NFE)

AF:

0.525

AC:

33215

AN:

63288

Other (OTH)

AF:

0.470

AC:

851

AN:

1812

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.527

Heterozygous variant carriers

1507

3015

4522

6030

7537

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

592

1184

1776

2368

2960

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.33

(source)

DANN

Benign

0.45

PhyloP100

-0.70

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over