rs12262943

Variant names:

• chr10-95756687-T-C
• rs12262943
• NM_001776.6:c.16+432T>C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001776.6(ENTPD1):​c.16+432T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 168,922 control chromosomes in the GnomAD database, including 507 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 0.057 (461 hom., cov: 31)
  • Exomes 𝑓: 0.045 (46 hom.)
• Consequence: ENTPD1 NM_001776.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD1	NM_001776.6	c.16+432T>C		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.16+432T>C		intron_variant	Intron 1 of 9	1	NM_001776.6	ENSP00000360248.4

Frequencies

GnomAD3 genomes AF: 0.0567 AC: 8617 AN: 152106 Hom.: 459 Cov.: 31

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.00518

Gnomad EAS AF: 0.164

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.0609

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00914

Gnomad OTH AF: 0.0427

GnomAD4 exome AF: 0.0448 AC: 748 AN: 16698 Hom.: 46 Cov.: 0 AF XY: 0.0497 AC XY: 463 AN XY: 9322

Gnomad4 AFR exome AF: 0.124

Gnomad4 AMR exome AF: 0.0756

Gnomad4 ASJ exome AF: 0.00345

Gnomad4 EAS exome AF: 0.169

Gnomad4 SAS exome AF: 0.123

Gnomad4 FIN exome AF: 0.0266

Gnomad4 NFE exome AF: 0.00989

Gnomad4 OTH exome AF: 0.0238

GnomAD4 genome AF: 0.0567 AC: 8637 AN: 152224 Hom.: 461 Cov.: 31 AF XY: 0.0609 AC XY: 4531 AN XY: 74440

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0622

Gnomad4 ASJ AF: 0.00518

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.135

Gnomad4 FIN AF: 0.0609

Gnomad4 NFE AF: 0.00916

Gnomad4 OTH AF: 0.0451

Alfa AF: 0.0261 Hom.: 27

Bravo AF: 0.0581

Asia WGS AF: 0.162 AC: 563 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	17
DANN	Benign	0.82

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

Publications

LitVar

Other links and lift over

dbSNP: rs12262943; hg19: chr10-97516444;