20-25226438-T-C

Variant names:

• chr20-25226438-T-C
• rs7453
• NM_001247.5:c.*841T>C

Variant summary

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

The NM_001247.5(ENTPD6):​c.*841T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 152,492 control chromosomes in the GnomAD database, including 22,204 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 0.52 (22153 hom., cov: 32)
  • Exomes 𝑓: 0.45 (51 hom.)
• Consequence: ENTPD6 NM_001247.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.251

Genes affected

ENTPD6 (HGNC:3368): (ectonucleoside triphosphate diphosphohydrolase 6) ENTPD6 is similar to E-type nucleotidases (NTPases). NTPases, such as CD39, mediate catabolism of extracellular nucleotides. ENTPD6 contains 4 apyrase-conserved regions which are characteristic of NTPases. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

ENSG00000279322 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ENTPD6	NM_001247.5	c.*841T>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000376652.9	NP_001238.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENTPD6	ENST00000376652.9	c.*841T>C		3_prime_UTR_variant	Exon 15 of 15	1	NM_001247.5	ENSP00000365840.4

Frequencies

GnomAD3 genomes AF: 0.524 AC: 79541 AN: 151890 Hom.: 22125 Cov.: 32

Gnomad AFR AF: 0.672

Gnomad AMI AF: 0.504

Gnomad AMR AF: 0.411

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.921

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.486

GnomAD4 exome AF: 0.450 AC: 218 AN: 484 Hom.: 51 Cov.: 0 AF XY: 0.486 AC XY: 141 AN XY: 290

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.444

Gnomad4 NFE exome AF: 0.425

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.524 AC: 79611 AN: 152008 Hom.: 22153 Cov.: 32 AF XY: 0.523 AC XY: 38854 AN XY: 74302

Gnomad4 AFR AF: 0.673

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.452

Gnomad4 OTH AF: 0.488

Alfa AF: 0.456 Hom.: 28676

Bravo AF: 0.525

Asia WGS AF: 0.691 AC: 2400 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.8
DANN	Benign	0.74
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs7453; hg19: chr20-25207074;