rs2073077

chr20-25215277-T-C

Variant summary

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

The NM_001247.5(ENTPD6):c.673+335T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,106 control chromosomes in the GnomAD database, including 5,440 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 0.24 (5440 hom., cov: 33)
• Consequence: ENTPD6 NM_001247.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.256

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ENTPD6	NM_001247.5	c.673+335T>C		intron_variant		ENST00000376652.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ENTPD6	ENST00000376652.9	c.673+335T>C		intron_variant		1	NM_001247.5	P4

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36053 AN: 151988 Hom.: 5425 Cov.: 33

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.237 AC: 36101 AN: 152106 Hom.: 5440 Cov.: 33 AF XY: 0.235 AC XY: 17495 AN XY: 74368

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.168

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.440

Gnomad4 SAS AF: 0.259

Gnomad4 FIN AF: 0.143

Gnomad4 NFE AF: 0.154

Gnomad4 OTH AF: 0.201

Alfa AF: 0.205 Hom.: 1101

Bravo AF: 0.245

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	3.0
Dann	Benign	0.65

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: rs2073077; hg19: chr20-25195913;