rs11598475

Positions:

• chr10-95861509-G-A

Variant summary

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

The NM_001776.6(ENTPD1):​c.1188+927G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 152,088 control chromosomes in the GnomAD database, including 6,315 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 0.27 (6315 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49

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]

ENSG00000270099 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.1188+927G>A		intron_variant		ENST00000371205.5	NP_001767.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD1	ENST00000371205.5	c.1188+927G>A		intron_variant		1	NM_001776.6	ENSP00000360248.4
ENSG00000270099	ENST00000491114.1	n.33+927G>A		intron_variant		5		ENSP00000473305.1

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40772 AN: 151970 Hom.: 6316 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.248

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 4

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.268 AC: 40776 AN: 152088 Hom.: 6315 Cov.: 32 AF XY: 0.267 AC XY: 19878 AN XY: 74352

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.384

Gnomad4 ASJ AF: 0.209

Gnomad4 EAS AF: 0.0417

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.245

Alfa AF: 0.301 Hom.: 912

Bravo AF: 0.271

Asia WGS AF: 0.132 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	14
DANN	Benign	0.63

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.080		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11598475; hg19: chr10-97621266;