chr3-40427763-G-T

Variant names:

• chr3-40427763-G-T
• rs6773917
• NM_001248.4:c.*255G>T

Variant summary

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

The NM_001248.4(ENTPD3):​c.*255G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.376 in 509,342 control chromosomes in the GnomAD database, including 38,650 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 0.41 (13827 hom., cov: 31)
  • Exomes 𝑓: 0.36 (24823 hom.)
• Consequence: ENTPD3 NM_001248.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.686

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:26710): (ENTPD3 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.569 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD3	NM_001248.4	c.*255G>T		3_prime_UTR_variant	Exon 11 of 11	ENST00000301825.8	NP_001239.2
ENTPD3	NM_001291960.2	c.*255G>T		3_prime_UTR_variant	Exon 11 of 11		NP_001278889.1
ENTPD3-AS1	NR_040100.1	n.265+23942C>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD3	ENST00000301825.8	c.*255G>T		3_prime_UTR_variant	Exon 11 of 11	1	NM_001248.4	ENSP00000301825.3

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62338 AN: 151830 Hom.: 13803 Cov.: 31

Gnomad AFR AF: 0.575

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.385

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.398

GnomAD4 exome AF: 0.361 AC: 129149 AN: 357394 Hom.: 24823 Cov.: 0 AF XY: 0.367 AC XY: 68818 AN XY: 187346

Gnomad4 AFR exome AF: 0.574

Gnomad4 AMR exome AF: 0.386

Gnomad4 ASJ exome AF: 0.391

Gnomad4 EAS exome AF: 0.526

Gnomad4 SAS exome AF: 0.472

Gnomad4 FIN exome AF: 0.375

Gnomad4 NFE exome AF: 0.306

Gnomad4 OTH exome AF: 0.371

GnomAD4 genome AF: 0.411 AC: 62412 AN: 151948 Hom.: 13827 Cov.: 31 AF XY: 0.416 AC XY: 30911 AN XY: 74276

Gnomad4 AFR AF: 0.575

Gnomad4 AMR AF: 0.385

Gnomad4 ASJ AF: 0.394

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.474

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.397

Alfa AF: 0.271 Hom.: 1109

Bravo AF: 0.420

Asia WGS AF: 0.508 AC: 1766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.63

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: rs6773917; hg19: chr3-40469254;