chr10-95751280-A-G

Position:

• chr10-95751280-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000453258.6(ENTPD1):​c.37+39287A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 152,038 control chromosomes in the GnomAD database, including 22,543 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 (22543 hom., cov: 32)
• Consequence: ENTPD1 ENST00000453258.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.840

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD1	NM_001098175.2	c.37+39287A>G		intron_variant
ENTPD1	XM_011540371.3	c.37+39287A>G		intron_variant
ENTPD1	XM_047426023.1	c.37+39287A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD1	ENST00000453258.6	c.37+39287A>G		intron_variant		1
ENTPD1-AS1	ENST00000669711.1	n.1351+4082T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81954 AN: 151920 Hom.: 22527 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.619

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.505

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

GnomAD4 genome AF: 0.539 AC: 82017 AN: 152038 Hom.: 22543 Cov.: 32 AF XY: 0.542 AC XY: 40261 AN XY: 74334

Gnomad4 AFR AF: 0.545

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.387

Gnomad4 EAS AF: 0.262

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.542

Gnomad4 OTH AF: 0.502

Alfa AF: 0.541 Hom.: 10189

Bravo AF: 0.543

Asia WGS AF: 0.439 AC: 1530 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7071836; hg19: chr10-97511037;