Genetic Variant ENTPD1:c.37+43773G>C (chr10-95755766-G-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The ENST00000453258.6(ENTPD1):c.37+43773G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000217 in 1,384,382 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)

Exomes 𝑓: 0.0000022 ( 0 hom. )

Consequence

ENTPD1
ENST00000453258.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.33

Publications

5 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:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.086177796).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	Protein	UniProt
ENTPD1	NM_001164178.1 link	c.52G>C	p.Glu18Gln	missense_variant, splice_region_variant	Exon 1 of 10	NP_001157650.1	P49961-6
ENTPD1	NM_001440935.1 link	c.52G>C	p.Glu18Gln	missense_variant, splice_region_variant	Exon 1 of 9	NP_001427864.1
ENTPD1	NM_001320916.1 link	c.52G>C	p.Glu18Gln	missense_variant, splice_region_variant	Exon 1 of 10	NP_001307845.1	P49961

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	Protein	UniProt
ENTPD1	ENST00000453258.6 link	c.37+43773G>C		intron_variant	Intron 1 of 9	1	ENSP00000390955.2	P49961-2
ENTPD1	ENST00000371207.8 link	c.52G>C	p.Glu18Gln	missense_variant, splice_region_variant	Exon 1 of 10	2	ENSP00000360250.3	P49961-6
ENTPD1	ENST00000543964.6 link	c.-181G>C		splice_region_variant	Exon 1 of 9	2	ENSP00000442968.1	P49961-5

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000705

AC:

AN:

141932

AF XY:

0.0000132

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.000119

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000217

AC:

AN:

1384382

Hom.:

Cov.:

AF XY:

0.00000439

AC XY:

AN XY:

683216

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

31580

American (AMR)

AF:

0.00

AC:

AN:

35698

Ashkenazi Jewish (ASJ)

AF:

0.0000397

AC:

AN:

25178

East Asian (EAS)

AF:

0.00

AC:

AN:

35730

South Asian (SAS)

AF:

0.00

AC:

AN:

79220

European-Finnish (FIN)

AF:

0.00

AC:

AN:

35000

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5696

European-Non Finnish (NFE)

AF:

9.27e-7

AC:

AN:

1078386

Other (OTH)

AF:

0.0000173

AC:

AN:

57894

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.408

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00000422

Hom.:

Bravo

AF:

0.00000378

ExAC

AF:

0.0000474

AC:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Uncertain

0.99

Eigen

Benign

-0.44

Eigen_PC

Benign

-0.48

FATHMM_MKL

Benign

0.34

LIST_S2

Benign

0.38

MetaRNN

Benign

0.086

MetaSVM

Benign

-1.0

PhyloP100

1.3

PrimateAI

Benign

0.30

PROVEAN

Benign

-0.45

REVEL

Benign

0.040

Sift

Benign

0.069

Sift4G

Benign

0.25

Vest4

0.16

MutPred

0.34

Loss of ubiquitination at K22 (P = 0.0613);

MVP

0.17

MPC

0.31

ClinPred

0.11

GERP RS

3.0

PromoterAI

-0.088

Neutral

(source)

gMVP

0.29

Mutation Taster

=266/34

polymorphism

(source)

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over