10-95755380-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.115

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 -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	UniProt
ENTPD1-AS1	NR_038444.1	n.2088C>T		non_coding_transcript_exon_variant	6/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000453258.6	c.37+43387G>A		intron_variant		1
ENTPD1-AS1	ENST00000669711.1	n.1333C>T		non_coding_transcript_exon_variant	6/7
ENTPD1-AS1	ENST00000416301.5	n.2067C>T		non_coding_transcript_exon_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76297 AN: 151988 Hom.: 19651 Cov.: 33

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.: 0 AF XY: 0.477 AC XY: 29386 AN XY: 61646

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.: 33 AF XY: 0.505 AC XY: 37530 AN XY: 74372

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:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Hereditary spastic paraplegia 64 Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Nov 29, 2022

- -

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 11, 2018

This variant is associated with the following publications: (PMID: 28302652) -

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

Other links and lift over

dbSNP: rs3814159; hg19: chr10-97515137;