Genetic Variant ENTPD3:c.*255G>T (chr3-40427763-G-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_001248.4(ENTPD3):c.*255G>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 0.376 in 509,342 control chromosomes in the GnomAD database, including 38,650 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 0.41 ( 13827 hom., cov: 31)

Exomes 𝑓: 0.36 ( 24823 hom. )

Consequence

ENTPD3
NM_001248.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.686

Publications

8 publications found

Variant links:

Genes affected

ENTPD3 (HGNC:3365): (ectonucleoside triphosphate diphosphohydrolase 3) This gene encodes a plasma membrane-bound divalent cation-dependent E-type nucleotidase. The encoded protein is involved in the regulation of extracellular levels of ATP by hydrolysis of it and other nucleotides. Multiple transcript variants have been described. [provided by RefSeq, May 2014]

ENTPD3 links:

ENTPD3-AS1 (HGNC:):

ENTPD3-AS1 links:

ENTPD3-AS1 (HGNC:26710): (ENTPD3 antisense RNA 1)

ENTPD3-AS1 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001248.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD3	NM_001248.4	MANE Select	c.*255G>T	3_prime_UTR	Exon 11 of 11	NP_001239.2	O75355-1
ENTPD3	NM_001291960.2		c.*255G>T	3_prime_UTR	Exon 11 of 11	NP_001278889.1	O75355-1
ENTPD3-AS1	NR_040100.1		n.265+23942C>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ENTPD3	ENST00000301825.8	TSL:1 MANE Select	c.*255G>T	3_prime_UTR	Exon 11 of 11	ENSP00000301825.3	O75355-1
ENTPD3-AS1	ENST00000425156.5	TSL:1	n.262+23942C>A	intron	N/A
ENTPD3	ENST00000900100.1		c.*255G>T	3_prime_UTR	Exon 10 of 10	ENSP00000570159.1

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

62338

AN:

151830

Hom.:

13803

Cov.:

show subpopulations

Gnomad AFR

AF:

0.575

Gnomad AMI

AF:

0.411

Gnomad AMR

AF:

0.385

Gnomad ASJ

AF:

0.394

Gnomad EAS

AF:

0.558

Gnomad SAS

AF:

0.474

Gnomad FIN

AF:

0.378

Gnomad MID

AF:

0.424

Gnomad NFE

AF:

0.307

Gnomad OTH

AF:

0.398

GnomAD4 exome

AF:

0.361

AC:

129149

AN:

357394

Hom.:

24823

Cov.:

AF XY:

0.367

AC XY:

68818

AN XY:

187346

show subpopulations

African (AFR)

AF:

0.574

AC:

6197

AN:

10796

American (AMR)

AF:

0.386

AC:

5709

AN:

14772

Ashkenazi Jewish (ASJ)

AF:

0.391

AC:

4434

AN:

11332

East Asian (EAS)

AF:

0.526

AC:

12638

AN:

24038

South Asian (SAS)

AF:

0.472

AC:

18077

AN:

38308

European-Finnish (FIN)

AF:

0.375

AC:

8119

AN:

21642

Middle Eastern (MID)

AF:

0.397

AC:

622

AN:

1566

European-Non Finnish (NFE)

AF:

0.306

AC:

65563

AN:

213952

Other (OTH)

AF:

0.371

AC:

7790

AN:

20988

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

3788

7576

11365

15153

18941

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

518

1036

1554

2072

2590

<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:

0.411

AC:

62412

AN:

151948

Hom.:

13827

Cov.:

AF XY:

0.416

AC XY:

30911

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.575

AC:

23836

AN:

41424

American (AMR)

AF:

0.385

AC:

5867

AN:

15258

Ashkenazi Jewish (ASJ)

AF:

0.394

AC:

1364

AN:

3466

East Asian (EAS)

AF:

0.558

AC:

2889

AN:

5182

South Asian (SAS)

AF:

0.474

AC:

2276

AN:

4802

European-Finnish (FIN)

AF:

0.378

AC:

3985

AN:

10538

Middle Eastern (MID)

AF:

0.415

AC:

122

AN:

294

European-Non Finnish (NFE)

AF:

0.307

AC:

20861

AN:

67962

Other (OTH)

AF:

0.397

AC:

837

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1819

3637

5456

7274

9093

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

584

1168

1752

2336

2920

<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:

0.305

Hom.:

2452

Bravo

AF:

0.420

Asia WGS

AF:

0.508

AC:

1766

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.74

(source)

DANN

Benign

0.63

PhyloP100

-0.69

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over