10-103273258-C-T

Position:

• chr10-103273258-C-T

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-25+2958G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,876 control chromosomes in the GnomAD database, including 21,096 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 (21096 hom., cov: 31)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

Genes affected

NT5C2 (HGNC:8022): (5'-nucleotidase, cytosolic II) This gene encodes a hydrolase that serves as an important role in cellular purine metabolism by acting primarily on inosine 5'-monophosphate and other purine nucleotides. [provided by RefSeq, Oct 2011]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.103273258C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000674696.1	c.-25+2958G>A		intron_variant				ENSP00000502679.1
NT5C2	ENST00000675326.1	c.-169+3896G>A		intron_variant				ENSP00000502205.1
NT5C2	ENST00000676428.1	c.-118+3896G>A		intron_variant				ENSP00000501689.1

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79373 AN: 151758 Hom.: 21073 Cov.: 31

Gnomad AFR AF: 0.607

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.523 AC: 79438 AN: 151876 Hom.: 21096 Cov.: 31 AF XY: 0.526 AC XY: 39071 AN XY: 74222

Gnomad4 AFR AF: 0.607

Gnomad4 AMR AF: 0.493

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.503

Alfa AF: 0.486 Hom.: 22038

Bravo AF: 0.517

Asia WGS AF: 0.546 AC: 1897 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.32
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1712517; hg19: chr10-105033015;