rs9332450

Positions:

• chr3-40416550-T-C

Variant summary

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

The NM_001248.4(ENTPD3):​c.831+477T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.418 in 152,088 control chromosomes in the GnomAD database, including 14,511 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 0.42 (14511 hom., cov: 32)
• Consequence: ENTPD3 NM_001248.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.90

Genes affected

ENTPD3 (HGNC:3365): (ectonucleoside triphosphate diphosphohydrolase 3) This gene encodes a plasma membrane-bound divalent cation-dependent E-type nucleotidase. The encoded protein is involved in the regulation of extracellular levels of ATP by hydrolysis of it and other nucleotides. Multiple transcript variants have been described. [provided by RefSeq, May 2014]

ENTPD3-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD3	NM_001248.4	c.831+477T>C		intron_variant		ENST00000301825.8	NP_001239.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD3	ENST00000301825.8	c.831+477T>C		intron_variant		1	NM_001248.4	ENSP00000301825.3

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63533 AN: 151970 Hom.: 14487 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.418 AC: 63607 AN: 152088 Hom.: 14511 Cov.: 32 AF XY: 0.424 AC XY: 31492 AN XY: 74358

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.387

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.400

Alfa AF: 0.333 Hom.: 15101

Bravo AF: 0.428

Asia WGS AF: 0.510 AC: 1773 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	0.0090
DANN	Benign	0.39

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: rs9332450; hg19: chr3-40458041;