20-25224395-C-G

Position:

• chr20-25224395-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001247.5(ENTPD6):​c.1243+238C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 378,204 control chromosomes in the GnomAD database, including 6,334 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 0.16 (2199 hom., cov: 33)
  • Exomes 𝑓: 0.18 (4135 hom.)
• Consequence: ENTPD6 NM_001247.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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]

ENTPD6 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD6	NM_001247.5	c.1243+238C>G		intron_variant		ENST00000376652.9	NP_001238.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD6	ENST00000376652.9	c.1243+238C>G		intron_variant		1	NM_001247.5	ENSP00000365840.4

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24158 AN: 152108 Hom.: 2195 Cov.: 33

Gnomad AFR AF: 0.0782

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.0982

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.152

GnomAD4 exome AF: 0.182 AC: 41181 AN: 225978 Hom.: 4135 Cov.: 2 AF XY: 0.179 AC XY: 21015 AN XY: 117170

Gnomad4 AFR exome AF: 0.0774

Gnomad4 AMR exome AF: 0.141

Gnomad4 ASJ exome AF: 0.0849

Gnomad4 EAS exome AF: 0.318

Gnomad4 SAS exome AF: 0.122

Gnomad4 FIN exome AF: 0.190

Gnomad4 NFE exome AF: 0.183

Gnomad4 OTH exome AF: 0.178

GnomAD4 genome AF: 0.159 AC: 24161 AN: 152226 Hom.: 2199 Cov.: 33 AF XY: 0.159 AC XY: 11844 AN XY: 74426

Gnomad4 AFR AF: 0.0780

Gnomad4 AMR AF: 0.164

Gnomad4 ASJ AF: 0.0982

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.154

Alfa AF: 0.0985 Hom.: 183

Bravo AF: 0.153

Asia WGS AF: 0.255 AC: 883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	15
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.23		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.23		Position offset: -8

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2179638; hg19: chr20-25205031;