chr20-25224395-C-G

Variant names:

• chr20-25224395-C-G
• rs2179638
• NM_001247.5:c.1243+238C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001247.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD6	NM_001247.5	MANE Select	c.1243+238C>G		intron	N/A	NP_001238.3
	ENTPD6	NM_001322378.2		c.1243+238C>G		intron	N/A	NP_001309307.2
	ENTPD6	NM_001317941.3		c.1240+238C>G		intron	N/A	NP_001304870.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENTPD6	ENST00000376652.9	TSL:1 MANE Select	c.1243+238C>G		intron	N/A	ENSP00000365840.4
	ENTPD6	ENST00000360031.6	TSL:1	c.1240+238C>G		intron	N/A	ENSP00000353131.2
	ENTPD6	ENST00000354989.10	TSL:1	c.1159+238C>G		intron	N/A	ENSP00000347084.6

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

African (AFR) AF: 0.0774 AC: 511 AN: 6602

American (AMR) AF: 0.141 AC: 943 AN: 6688

Ashkenazi Jewish (ASJ) AF: 0.0849 AC: 698 AN: 8224

East Asian (EAS) AF: 0.318 AC: 5827 AN: 18300

South Asian (SAS) AF: 0.122 AC: 1640 AN: 13472

European-Finnish (FIN) AF: 0.190 AC: 3300 AN: 17352

Middle Eastern (MID) AF: 0.0903 AC: 99 AN: 1096

European-Non Finnish (NFE) AF: 0.183 AC: 25641 AN: 140100

Other (OTH) AF: 0.178 AC: 2522 AN: 14144

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

African (AFR) AF: 0.0780 AC: 3240 AN: 41554

American (AMR) AF: 0.164 AC: 2513 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0982 AC: 341 AN: 3472

East Asian (EAS) AF: 0.329 AC: 1695 AN: 5156

South Asian (SAS) AF: 0.124 AC: 597 AN: 4830

European-Finnish (FIN) AF: 0.195 AC: 2069 AN: 10602

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13099 AN: 67992

Other (OTH) AF: 0.154 AC: 325 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	15
DANN	Benign	0.73
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2179638; hg19: chr20-25205031;