10-95756521-GT-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001776.6(ENTPD1):c.16+273del variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.54 (22521 hom., cov: 0)
  • Exomes 𝑓: 0.52 (44515 hom.)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.335

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-AS1 (HGNC:45203): (ENTPD1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 10-95756521-GT-G is Benign according to our data. Variant chr10-95756521-GT-G is described in ClinVar as [Benign]. Clinvar id is 1274919.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001776.6	c.16+273del		intron_variant		ENST00000371205.5
ENTPD1-AS1	NR_038444.1	n.946del		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000371205.5	c.16+273del		intron_variant		1	NM_001776.6	P1
ENTPD1-AS1	ENST00000669711.1	n.848+95del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81814 AN: 151650 Hom.: 22505 Cov.: 0

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.620

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.504

GnomAD4 exome AF: 0.517 AC: 164155 AN: 317616 Hom.: 44515 Cov.: 0 AF XY: 0.517 AC XY: 86607 AN XY: 167476

Gnomad4 AFR exome AF: 0.542

Gnomad4 AMR exome AF: 0.653

Gnomad4 ASJ exome AF: 0.379

Gnomad4 EAS exome AF: 0.306

Gnomad4 SAS exome AF: 0.552

Gnomad4 FIN exome AF: 0.527

Gnomad4 NFE exome AF: 0.534

Gnomad4 OTH exome AF: 0.508

GnomAD4 genome AF: 0.539 AC: 81877 AN: 151768 Hom.: 22521 Cov.: 0 AF XY: 0.542 AC XY: 40165 AN XY: 74136

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.501

Alfa AF: 0.432 Hom.: 1247

Bravo AF: 0.543

Asia WGS AF: 0.438 AC: 1527 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

Apr 16, 2021

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs75745138; hg19: chr10-97516278;