chr10-95810654-G-C

Variant names:

• chr10-95810654-G-C
• rs4074424
• NM_001776.6:c.17-12583G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001312654.1(ENTPD1):​c.-333G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,094 control chromosomes in the GnomAD database, including 22,552 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 0.54 (22552 hom., cov: 33)
• Consequence: ENTPD1 NM_001312654.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.66
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.617 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001312654.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	NM_001776.6	MANE Select	c.17-12583G>C		intron	N/A	NP_001767.3
	ENTPD1	NM_001312654.1		c.-333G>C		5_prime_UTR	Exon 2 of 10	NP_001299583.1	P49961-5
	ENTPD1	NM_001440932.1		c.95-12583G>C		intron	N/A	NP_001427861.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000371205.5	TSL:1 MANE Select	c.17-12583G>C		intron	N/A	ENSP00000360248.4	P49961-1
	ENTPD1	ENST00000453258.6	TSL:1	c.38-12583G>C		intron	N/A	ENSP00000390955.2	P49961-2
	ENTPD1	ENST00000635076.1	TSL:1	n.17-12583G>C		intron	N/A	ENSP00000489250.1	A0A0U1RQZ5

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81949 AN: 151976 Hom.: 22529 Cov.: 33

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.622

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.539 AC: 82022 AN: 152094 Hom.: 22552 Cov.: 33 AF XY: 0.541 AC XY: 40252 AN XY: 74338

African (AFR) AF: 0.545 AC: 22606 AN: 41500

American (AMR) AF: 0.627 AC: 9587 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.386 AC: 1340 AN: 3472

East Asian (EAS) AF: 0.262 AC: 1355 AN: 5166

South Asian (SAS) AF: 0.563 AC: 2715 AN: 4820

European-Finnish (FIN) AF: 0.557 AC: 5870 AN: 10548

Middle Eastern (MID) AF: 0.384 AC: 113 AN: 294

European-Non Finnish (NFE) AF: 0.541 AC: 36811 AN: 67984

Other (OTH) AF: 0.501 AC: 1060 AN: 2114

Alfa AF: 0.415 Hom.: 1158

Bravo AF: 0.543

Asia WGS AF: 0.439 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.28
DANN	Benign	0.45
PhyloP100		-1.7
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: rs4074424; hg19: chr10-97570411;