chr10-95858823-T-C

Variant names:

• chr10-95858823-T-C
• rs3181121
• NM_001776.6:c.1075-1646T>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.1075-1646T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0731 in 152,128 control chromosomes in the GnomAD database, including 448 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 (448 hom., cov: 32)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710
• 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)

ENSG00000240527 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0925 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.1075-1646T>C		intron_variant	Intron 7 of 9	ENST00000371205.5	NP_001767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5	c.1075-1646T>C		intron_variant	Intron 7 of 9	1	NM_001776.6	ENSP00000360248.4

Frequencies

GnomAD3 genomes AF: 0.0731 AC: 11115 AN: 152010 Hom.: 449 Cov.: 32

Gnomad AFR AF: 0.0950

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0631

Gnomad ASJ AF: 0.0280

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0905

Gnomad FIN AF: 0.0730

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0645

Gnomad OTH AF: 0.0650

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

GnomAD4 genome AF: 0.0731 AC: 11123 AN: 152128 Hom.: 448 Cov.: 32 AF XY: 0.0730 AC XY: 5434 AN XY: 74388

African (AFR) AF: 0.0949 AC: 3940 AN: 41502

American (AMR) AF: 0.0631 AC: 964 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0280 AC: 97 AN: 3464

East Asian (EAS) AF: 0.0471 AC: 244 AN: 5178

South Asian (SAS) AF: 0.0899 AC: 433 AN: 4816

European-Finnish (FIN) AF: 0.0730 AC: 773 AN: 10588

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

European-Non Finnish (NFE) AF: 0.0646 AC: 4388 AN: 67976

Other (OTH) AF: 0.0643 AC: 136 AN: 2114

Alfa AF: 0.0646 Hom.: 628

Bravo AF: 0.0721

Asia WGS AF: 0.0640 AC: 224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.56
PhyloP100		0.071
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: rs3181121; hg19: chr10-97618580;