rs4918972

chr10-95819464-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001776.6(ENTPD1):c.17-3773G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.269 in 151,984 control chromosomes in the GnomAD database, including 6,347 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6347 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001776.6	c.17-3773G>A		intron_variant		ENST00000371205.5
ENTPD1-AS1	NR_038444.1	n.533+27928C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000371205.5	c.17-3773G>A		intron_variant		1	NM_001776.6	P1
ENTPD1-AS1	ENST00000669711.1	n.444-34219C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.269 AC: 40898 AN: 151868 Hom.: 6349 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.0422

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.223

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.248

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

GnomAD4 genome AF: 0.269 AC: 40899 AN: 151984 Hom.: 6347 Cov.: 32 AF XY: 0.268 AC XY: 19926 AN XY: 74288

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.245

Alfa AF: 0.296 Hom.: 921

Bravo AF: 0.272

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.60
Dann	Benign	0.42

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: rs4918972; hg19: chr10-97579221;