chr10-99673635-G-A

Position:

• chr10-99673635-G-A

Variant summary

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

The NM_020354.5(ENTPD7):​c.192-5626G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.84 in 152,234 control chromosomes in the GnomAD database, including 53,955 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 0.84 (53955 hom., cov: 33)
• Consequence: ENTPD7 NM_020354.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

ENTPD7 (HGNC:19745): (ectonucleoside triphosphate diphosphohydrolase 7) This gene encodes a purine-converting ectoenzyme which belongs to the ecto-nucleoside triphosphate diphosphohydrolase (E-NTPDase) family. The encoded protein hydrolyzes extracellular nucleoside triphosphates (UTP, GTP, and CTP) to nucleoside monophosphates as part of a purinergic signaling pathway. It contains two transmembrane domains at the N- and C-termini and a large, hydrophobic catalytic domain located in between. This gene affects oxidative stress as well as DNA damage and is a mediator of senescence. [provided by RefSeq, Mar 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ENTPD7	NM_020354.5	c.192-5626G>A		intron_variant		ENST00000370489.5	NP_065087.1
ENTPD7	NM_001349962.2	c.198-5626G>A		intron_variant			NP_001336891.1
ENTPD7	NM_001349963.2	c.192-5626G>A		intron_variant			NP_001336892.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENTPD7	ENST00000370489.5	c.192-5626G>A		intron_variant		1	NM_020354.5	ENSP00000359520	P1

Frequencies

GnomAD3 genomes AF: 0.840 AC: 127799 AN: 152116 Hom.: 53925 Cov.: 33

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.873

Gnomad ASJ AF: 0.830

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.889

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.878

Gnomad OTH AF: 0.852

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

GnomAD4 genome AF: 0.840 AC: 127885 AN: 152234 Hom.: 53955 Cov.: 33 AF XY: 0.841 AC XY: 62588 AN XY: 74442

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.873

Gnomad4 ASJ AF: 0.830

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.889

Gnomad4 NFE AF: 0.878

Gnomad4 OTH AF: 0.849

Alfa AF: 0.868 Hom.: 96267

Bravo AF: 0.835

Asia WGS AF: 0.818 AC: 2849 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.9
DANN	Benign	0.64

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: rs911541; hg19: chr10-101433392;