Genetic Variant NM_001248.4:c.*255G>A (chr3-40427763-G-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001248.4(ENTPD3):c.*255G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000837 in 358,352 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: 31)

Exomes 𝑓: 0.0000084 ( 0 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:

EIF1B-AS1 (HGNC:):

EIF1B-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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein
ENTPD3	NM_001248.4 link	c.*255G>A	3_prime_UTR_variant	Exon 11 of 11	ENST00000301825.8	NP_001239.2
ENTPD3	NM_001291960.2 link	c.*255G>A	3_prime_UTR_variant	Exon 11 of 11		NP_001278889.1
ENTPD3-AS1	NR_040100.1 link	n.265+23942C>T	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD3	ENST00000301825.8 link	c.*255G>A		3_prime_UTR_variant	Exon 11 of 11	1	NM_001248.4	ENSP00000301825.3

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000837

AC:

AN:

358352

Hom.:

Cov.:

AF XY:

0.0000106

AC XY:

AN XY:

187856

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10824

American (AMR)

AF:

0.00

AC:

AN:

14800

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11354

East Asian (EAS)

AF:

0.00

AC:

AN:

24120

South Asian (SAS)

AF:

0.00

AC:

AN:

38384

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21726

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1574

European-Non Finnish (NFE)

AF:

0.0000140

AC:

AN:

214524

Other (OTH)

AF:

0.00

AC:

AN:

21046

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

2452

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.8

(source)

DANN

Benign

0.89

PhyloP100

-0.69

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over