dbSNP rs11188513: ENTPD1:c.*6881C>T (chr10-95873264-C-T) – 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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

21 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=-0.9).

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 rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6 link	c.*6881C>T		3_prime_UTR_variant	Exon 10 of 10	ENST00000371205.5	NP_001767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5 link	c.*6881C>T		3_prime_UTR_variant	Exon 10 of 10	1	NM_001776.6	ENSP00000360248.4
ENSG00000270099	ENST00000491114.1 link	n.171+8403C>T		intron_variant	Intron 2 of 6	5		ENSP00000473305.1

Frequencies

GnomAD3 genomes

AF:

0.656

AC:

99694

AN:

151930

Hom.:

33284

Cov.:

show subpopulations

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.:

AF XY:

0.661

AC XY:

254219

AN XY:

384686

show subpopulations

African (AFR)

AF:

0.682

AC:

10767

AN:

15782

American (AMR)

AF:

0.748

AC:

736

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.569

AC:

2929

AN:

5150

East Asian (EAS)

AF:

0.247

AC:

896

AN:

3630

South Asian (SAS)

AF:

0.624

AC:

10269

AN:

16458

European-Finnish (FIN)

AF:

0.663

AC:

183

AN:

276

Middle Eastern (MID)

AF:

0.573

AC:

928

AN:

1620

European-Non Finnish (NFE)

AF:

0.665

AC:

506549

AN:

761856

Other (OTH)

AF:

0.633

AC:

17289

AN:

27296

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

10688

21376

32064

42752

53440

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

17942

35884

53826

71768

89710

<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:

0.656

AC:

99785

AN:

152048

Hom.:

33319

Cov.:

AF XY:

0.658

AC XY:

48916

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.675

AC:

27990

AN:

41448

American (AMR)

AF:

0.724

AC:

11060

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.559

AC:

1938

AN:

3468

East Asian (EAS)

AF:

0.266

AC:

1379

AN:

5178

South Asian (SAS)

AF:

0.618

AC:

2982

AN:

4824

European-Finnish (FIN)

AF:

0.711

AC:

7509

AN:

10566

Middle Eastern (MID)

AF:

0.565

AC:

166

AN:

294

European-Non Finnish (NFE)

AF:

0.659

AC:

44785

AN:

67972

Other (OTH)

AF:

0.628

AC:

1322

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1726

3453

5179

6906

8632

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

786

1572

2358

3144

3930

<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:

0.656

Hom.:

98302

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

(source)

DANN

Benign

0.53

PhyloP100

-1.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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