chr3-40416550-T-C

Variant names:

• chr3-40416550-T-C
• rs9332450
• NM_001248.4:c.831+477T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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]

EIF1B-AS1 (HGNC:):

ENTPD3-AS1 (HGNC:26710): (ENTPD3 antisense RNA 1)

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 = 0.595 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD3	NM_001248.4	c.831+477T>C		intron_variant	Intron 7 of 10	ENST00000301825.8	NP_001239.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD3	ENST00000301825.8	c.831+477T>C		intron_variant	Intron 7 of 10	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

African (AFR) AF: 0.601 AC: 24948 AN: 41488

American (AMR) AF: 0.387 AC: 5914 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1380 AN: 3472

East Asian (EAS) AF: 0.558 AC: 2884 AN: 5166

South Asian (SAS) AF: 0.475 AC: 2283 AN: 4810

European-Finnish (FIN) AF: 0.378 AC: 3996 AN: 10574

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.307 AC: 20864 AN: 67976

Other (OTH) AF: 0.400 AC: 844 AN: 2112

Alfa AF: 0.346 Hom.: 37621

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
PhyloP100		-2.9
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: rs9332450; hg19: chr3-40458041;