Genetic Variant ENTPD1:c.37+44161A>C (chr10-95756154-A-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_001164178.1(ENTPD1):c.52+388A>C variant causes a intron change. The variant allele was found at a frequency of 0.00164 in 1,556,112 control chromosomes in the GnomAD database, including 64 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.0025 ( 18 hom., cov: 31)

Exomes 𝑓: 0.0016 ( 46 hom. )

Consequence

ENTPD1
NM_001164178.1 intron

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 4.18

Publications

0 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:

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.33).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0562 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001164178.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD1	NM_001164178.1	c.52+388A>C	intron	N/A	NP_001157650.1	P49961-6
ENTPD1	NM_001098175.2	c.37+44161A>C	intron	N/A	NP_001091645.1	P49961-2
ENTPD1	NM_001440933.1	c.37+44161A>C	intron	N/A	NP_001427862.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD1	ENST00000453258.6	TSL:1	c.37+44161A>C	intron	N/A	ENSP00000390955.2	P49961-2
ENTPD1	ENST00000953039.1		c.-86A>C	5_prime_UTR	Exon 1 of 9	ENSP00000623098.1
ENTPD1	ENST00000953040.1		c.-86A>C	5_prime_UTR	Exon 1 of 10	ENSP00000623099.1

Frequencies

GnomAD3 genomes

AF:

0.00251

AC:

381

AN:

151668

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000970

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00118

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.0617

Gnomad SAS

AF:

0.00499

Gnomad FIN

AF:

0.0000950

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000132

Gnomad OTH

AF:

0.00288

GnomAD4 exome

AF:

0.00155

AC:

2177

AN:

1404326

Hom.:

Cov.:

AF XY:

0.00159

AC XY:

1104

AN XY:

693468

show subpopulations

African (AFR)

AF:

0.0000631

AC:

AN:

31706

American (AMR)

AF:

0.000304

AC:

AN:

36218

Ashkenazi Jewish (ASJ)

AF:

0.000238

AC:

AN:

25218

East Asian (EAS)

AF:

0.0452

AC:

1632

AN:

36114

South Asian (SAS)

AF:

0.00242

AC:

193

AN:

79636

European-Finnish (FIN)

AF:

0.000160

AC:

AN:

50024

Middle Eastern (MID)

AF:

0.000376

AC:

AN:

5326

European-Non Finnish (NFE)

AF:

0.0000453

AC:

AN:

1081924

Other (OTH)

AF:

0.00471

AC:

274

AN:

58160

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

120

240

359

479

599

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

114

152

190

<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:

0.00251

AC:

381

AN:

151786

Hom.:

Cov.:

AF XY:

0.00280

AC XY:

208

AN XY:

74176

show subpopulations

African (AFR)

AF:

0.0000967

AC:

AN:

41356

American (AMR)

AF:

0.00118

AC:

AN:

15224

Ashkenazi Jewish (ASJ)

AF:

0.000289

AC:

AN:

3466

East Asian (EAS)

AF:

0.0618

AC:

318

AN:

5146

South Asian (SAS)

AF:

0.00500

AC:

AN:

4802

European-Finnish (FIN)

AF:

0.0000950

AC:

AN:

10530

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.000132

AC:

AN:

67954

Other (OTH)

AF:

0.00285

AC:

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.000738

Hom.:

Bravo

AF:

0.00275

Asia WGS

AF:

0.0280

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

Hereditary spastic paraplegia (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.33

CADD

Benign

(source)

DANN

Benign

0.94

PhyloP100

4.2

PromoterAI

0.25

Neutral

(source)

Mutation Taster

=299/1

polymorphism

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over