10-95819464-G-A

Variant names:

• chr10-95819464-G-A
• rs4918972
• NM_001776.6:c.17-3773G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001776.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	NM_001776.6	MANE Select	c.17-3773G>A		intron	N/A	NP_001767.3
	ENTPD1	NM_001440932.1		c.95-3773G>A		intron	N/A	NP_001427861.1
	ENTPD1	NM_001164178.1		c.53-3773G>A		intron	N/A	NP_001157650.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000371205.5	TSL:1 MANE Select	c.17-3773G>A		intron	N/A	ENSP00000360248.4
	ENTPD1	ENST00000453258.6	TSL:1	c.38-3773G>A		intron	N/A	ENSP00000390955.2
	ENTPD1	ENST00000635076.1	TSL:1	n.17-3773G>A		intron	N/A	ENSP00000489250.1

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

African (AFR) AF: 0.140 AC: 5789 AN: 41458

American (AMR) AF: 0.383 AC: 5846 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3472

East Asian (EAS) AF: 0.0417 AC: 216 AN: 5178

South Asian (SAS) AF: 0.220 AC: 1058 AN: 4816

European-Finnish (FIN) AF: 0.311 AC: 3279 AN: 10556

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.339 AC: 23029 AN: 67936

Other (OTH) AF: 0.245 AC: 518 AN: 2114

Alfa AF: 0.306 Hom.: 9780

Bravo AF: 0.272

Asia WGS AF: 0.133 AC: 464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.60
DANN	Benign	0.42
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4918972; hg19: chr10-97579221;