rs7093453

Variant names:

• chr10-95811818-C-T
• rs7093453
• NM_001776.6:c.17-11419C>T

Variant summary

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

The NM_001776.6(ENTPD1):​c.17-11419C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0732 in 152,266 control chromosomes in the GnomAD database, including 452 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 0.073 (452 hom., cov: 33)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0860
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.094 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.17-11419C>T		intron_variant	Intron 1 of 9	ENST00000371205.5	NP_001767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5	c.17-11419C>T		intron_variant	Intron 1 of 9	1	NM_001776.6	ENSP00000360248.4

Frequencies

GnomAD3 genomes AF: 0.0732 AC: 11134 AN: 152148 Hom.: 453 Cov.: 33

Gnomad AFR AF: 0.0966

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0632

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0452

Gnomad SAS AF: 0.0886

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0640

Gnomad OTH AF: 0.0632

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

GnomAD4 genome AF: 0.0732 AC: 11144 AN: 152266 Hom.: 452 Cov.: 33 AF XY: 0.0732 AC XY: 5445 AN XY: 74424

African (AFR) AF: 0.0965 AC: 4011 AN: 41546

American (AMR) AF: 0.0632 AC: 967 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3470

East Asian (EAS) AF: 0.0457 AC: 237 AN: 5190

South Asian (SAS) AF: 0.0880 AC: 425 AN: 4828

European-Finnish (FIN) AF: 0.0733 AC: 777 AN: 10600

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0640 AC: 4351 AN: 68020

Other (OTH) AF: 0.0625 AC: 132 AN: 2112

Alfa AF: 0.0713 Hom.: 68

Bravo AF: 0.0723

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.62
PhyloP100		-0.086
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: rs7093453; hg19: chr10-97571575;