10-95758942-G-C

Variant names:

• chr10-95758942-G-C
• rs1418709
• NM_001776.6:c.16+2687G>C

Variant summary

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

The NM_001776.6(ENTPD1):​c.16+2687G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,984 control chromosomes in the GnomAD database, including 19,649 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 0.50 (19649 hom., cov: 31)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.588 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	NM_001776.6	MANE Select	c.16+2687G>C		intron	N/A	NP_001767.3
	ENTPD1	NM_001440932.1		c.94+2166G>C		intron	N/A	NP_001427861.1
	ENTPD1	NM_001164178.1		c.52+3176G>C		intron	N/A	NP_001157650.1	P49961-6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000371205.5	TSL:1 MANE Select	c.16+2687G>C		intron	N/A	ENSP00000360248.4	P49961-1
	ENTPD1	ENST00000453258.6	TSL:1	c.37+46949G>C		intron	N/A	ENSP00000390955.2	P49961-2
	ENTPD1	ENST00000635076.1	TSL:1	n.16+2687G>C		intron	N/A	ENSP00000489250.1	A0A0U1RQZ5

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76231 AN: 151866 Hom.: 19634 Cov.: 31

Gnomad AFR AF: 0.517

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: 0.360

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.502 AC: 76295 AN: 151984 Hom.: 19649 Cov.: 31 AF XY: 0.505 AC XY: 37499 AN XY: 74290

African (AFR) AF: 0.518 AC: 21449 AN: 41430

American (AMR) AF: 0.598 AC: 9133 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3470

East Asian (EAS) AF: 0.261 AC: 1347 AN: 5154

South Asian (SAS) AF: 0.553 AC: 2662 AN: 4814

European-Finnish (FIN) AF: 0.519 AC: 5476 AN: 10556

Middle Eastern (MID) AF: 0.349 AC: 102 AN: 292

European-Non Finnish (NFE) AF: 0.492 AC: 33454 AN: 67974

Other (OTH) AF: 0.464 AC: 980 AN: 2110

Alfa AF: 0.375 Hom.: 1049

Bravo AF: 0.507

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	12
DANN	Benign	0.65
PhyloP100		0.41
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: rs1418709; hg19: chr10-97518699; COSMIC: COSV104428146;