10-95754702-G-A

Variant names:

• chr10-95754702-G-A
• rs3176894
• ENST00000453258.6:c.37+42709G>A

Variant summary

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

The NM_001098175.2(ENTPD1):​c.37+42709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.829 in 152,218 control chromosomes in the GnomAD database, including 52,954 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 0.83 (52952 hom., cov: 33)
  • Exomes 𝑓: 1.0 (2 hom.)
• Consequence: ENTPD1 NM_001098175.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001098175.2. 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_001098175.2		c.37+42709G>A		intron	N/A	NP_001091645.1
	ENTPD1	NM_001440933.1		c.37+42709G>A		intron	N/A	NP_001427862.1
	ENTPD1	NM_001440934.1		c.37+42709G>A		intron	N/A	NP_001427863.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD1	ENST00000453258.6	TSL:1	c.37+42709G>A		intron	N/A	ENSP00000390955.2
	ENTPD1-AS1	ENST00000416301.5	TSL:2	n.2745C>T		non_coding_transcript_exon	Exon 6 of 6
	ENTPD1-AS1	ENST00000669711.1		n.1351+660C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.829 AC: 126126 AN: 152096 Hom.: 52924 Cov.: 33

Gnomad AFR AF: 0.920

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.810

Gnomad OTH AF: 0.832

GnomAD4 exome AF: 1.00 AC: 4 AN: 4 Hom.: 2 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 1.00 AC: 4 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.829 AC: 126203 AN: 152214 Hom.: 52952 Cov.: 33 AF XY: 0.826 AC XY: 61492 AN XY: 74410

African (AFR) AF: 0.920 AC: 38213 AN: 41544

American (AMR) AF: 0.857 AC: 13114 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.812 AC: 2819 AN: 3470

East Asian (EAS) AF: 0.438 AC: 2266 AN: 5174

South Asian (SAS) AF: 0.777 AC: 3745 AN: 4822

European-Finnish (FIN) AF: 0.770 AC: 8153 AN: 10584

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.810 AC: 55112 AN: 68000

Other (OTH) AF: 0.827 AC: 1746 AN: 2112

Alfa AF: 0.772 Hom.: 2297

Bravo AF: 0.838

Asia WGS AF: 0.633 AC: 2202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.37
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3176894; hg19: chr10-97514459;