10-95712168-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000453258.6(ENTPD1):c.37+175T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 152,040 control chromosomes in the GnomAD database, including 10,121 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.35 (10121 hom., cov: 32)
• Consequence: ENTPD1 ENST00000453258.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.238

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BP6: Variant 10-95712168-T-C is Benign according to our data. Variant chr10-95712168-T-C is described in ClinVar as [Benign]. Clinvar id is 1292728.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001098175.2	c.37+175T>C		intron_variant
ENTPD1	XM_011540371.3	c.37+175T>C		intron_variant
ENTPD1	XM_047426023.1	c.37+175T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000453258.6	c.37+175T>C		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53735 AN: 151922 Hom.: 10107 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.354 AC: 53799 AN: 152040 Hom.: 10121 Cov.: 32 AF XY: 0.352 AC XY: 26144 AN XY: 74326

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.696

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.370

Alfa AF: 0.330 Hom.: 1075

Bravo AF: 0.357

Asia WGS AF: 0.514 AC: 1786 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	8.3
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12244559; hg19: chr10-97471925;