Variant chr10-95823211-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001776.6(ENTPD1):c.17-26T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 1,612,854 control chromosomes in the GnomAD database, including 402 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.014 ( 27 hom., cov: 33)

Exomes 𝑓: 0.019 ( 375 hom. )

Consequence

ENTPD1
NM_001776.6 intron

Scores

Clinical Significance

Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.452

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=-0.6).

BP6

Variant 10-95823211-T-C is Benign according to our data. Variant chr10-95823211-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 1342044.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0145 (2207/152364) while in subpopulation SAS AF= 0.0213 (103/4830). AF 95% confidence interval is 0.0199. There are 27 homozygotes in gnomad4. There are 1068 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 27 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD1	NM_001776.6 linkuse as main transcript	c.17-26T>C		intron_variant		ENST00000371205.5	NP_001767.3
ENTPD1-AS1	NR_038444.1 linkuse as main transcript	n.533+24181A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5 linkuse as main transcript	c.17-26T>C		intron_variant		1	NM_001776.6	ENSP00000360248	P1	P49961-1
ENTPD1-AS1	ENST00000669711.1 linkuse as main transcript	n.444-37966A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0145

AC:

2205

AN:

152246

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00316

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.00890

Gnomad ASJ

AF:

0.0253

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.0209

Gnomad FIN

AF:

0.0233

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.0208

Gnomad OTH

AF:

0.0110

GnomAD3 exomes

AF:

0.0150

AC:

3762

AN:

251332

Hom.:

AF XY:

0.0157

AC XY:

2135

AN XY:

135866

show subpopulations

Gnomad AFR exome

AF:

0.00351

Gnomad AMR exome

AF:

0.00547

Gnomad ASJ exome

AF:

0.0252

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0174

Gnomad FIN exome

AF:

0.0197

Gnomad NFE exome

AF:

0.0195

Gnomad OTH exome

AF:

0.0129

GnomAD4 exome

AF:

0.0194

AC:

28291

AN:

1460490

Hom.:

375

Cov.:

AF XY:

0.0193

AC XY:

14031

AN XY:

726548

show subpopulations

Gnomad4 AFR exome

AF:

0.00281

Gnomad4 AMR exome

AF:

0.00584

Gnomad4 ASJ exome

AF:

0.0257

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.0173

Gnomad4 FIN exome

AF:

0.0190

Gnomad4 NFE exome

AF:

0.0212

Gnomad4 OTH exome

AF:

0.0188

GnomAD4 genome

AF:

0.0145

AC:

2207

AN:

152364

Hom.:

Cov.:

AF XY:

0.0143

AC XY:

1068

AN XY:

74504

show subpopulations

Gnomad4 AFR

AF:

0.00315

Gnomad4 AMR

AF:

0.00889

Gnomad4 ASJ

AF:

0.0253

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.0213

Gnomad4 FIN

AF:

0.0233

Gnomad4 NFE

AF:

0.0208

Gnomad4 OTH

AF:

0.0109

Alfa

AF:

0.0187

Hom.:

Bravo

AF:

0.0127

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	May 11, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.84

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

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