Variant chr10-95755380-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000453258.6(ENTPD1):c.37+43387G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 270,644 control chromosomes in the GnomAD database, including 33,843 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 19666 hom., cov: 33)

Exomes 𝑓: 0.48 ( 14177 hom. )

Consequence

ENTPD1
ENST00000453258.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.115

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.73).

BP6

Variant 10-95755380-G-A is Benign according to our data. Variant chr10-95755380-G-A is described in ClinVar as [Benign]. Clinvar id is 1249702.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD1-AS1	NR_038444.1 linkuse as main transcript	n.2088C>T		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	Protein	UniProt
ENTPD1	ENST00000453258.6 linkuse as main transcript	c.37+43387G>A	intron_variant		1	ENSP00000390955	P49961-2
ENTPD1-AS1	ENST00000669711.1 linkuse as main transcript	n.1333C>T	non_coding_transcript_exon_variant	6/7
ENTPD1-AS1	ENST00000416301.5 linkuse as main transcript	n.2067C>T	non_coding_transcript_exon_variant	6/6	2

Frequencies

GnomAD3 genomes

AF:

0.502

AC:

76297

AN:

151988

Hom.:

19651

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.596

Gnomad AMR

AF:

0.598

Gnomad ASJ

AF:

0.331

Gnomad EAS

AF:

0.261

Gnomad SAS

AF:

0.555

Gnomad FIN

AF:

0.519

Gnomad MID

AF:

0.361

Gnomad NFE

AF:

0.492

Gnomad OTH

AF:

0.466

GnomAD4 exome

AF:

0.477

AC:

56569

AN:

118538

Hom.:

14177

Cov.:

AF XY:

0.477

AC XY:

29386

AN XY:

61646

show subpopulations

Gnomad4 AFR exome

AF:

0.506

Gnomad4 AMR exome

AF:

0.616

Gnomad4 ASJ exome

AF:

0.327

Gnomad4 EAS exome

AF:

0.302

Gnomad4 SAS exome

AF:

0.511

Gnomad4 FIN exome

AF:

0.493

Gnomad4 NFE exome

AF:

0.487

Gnomad4 OTH exome

AF:

0.487

GnomAD4 genome

AF:

0.502

AC:

76361

AN:

152106

Hom.:

19666

Cov.:

AF XY:

0.505

AC XY:

37530

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.518

Gnomad4 AMR

AF:

0.598

Gnomad4 ASJ

AF:

0.331

Gnomad4 EAS

AF:

0.261

Gnomad4 SAS

AF:

0.553

Gnomad4 FIN

AF:

0.519

Gnomad4 NFE

AF:

0.492

Gnomad4 OTH

AF:

0.464

Alfa

AF:

0.487

Hom.:

14305

Bravo

AF:

0.507

Asia WGS

AF:

0.432

AC:

1504

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 11, 2018	This variant is associated with the following publications: (PMID: 28302652) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Hereditary spastic paraplegia 64

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 29, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

9.9

DANN

Benign

0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over