chr10-103261506-G-A

Position:

• chr10-103261506-G-A

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-25+14710C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,004 control chromosomes in the GnomAD database, including 15,107 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 0.44 (15107 hom., cov: 32)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.130

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000674696.1	c.-25+14710C>T		intron_variant				ENSP00000502679	P1
NT5C2	ENST00000675326.1	c.-169+15648C>T		intron_variant				ENSP00000502205	P1
NT5C2	ENST00000676428.1	c.-118+15648C>T		intron_variant				ENSP00000501689	P1

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67573 AN: 151886 Hom.: 15103 Cov.: 32

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.450

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.475

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.445 AC: 67605 AN: 152004 Hom.: 15107 Cov.: 32 AF XY: 0.448 AC XY: 33272 AN XY: 74294

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.450

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.457

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.475

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.435

Alfa AF: 0.403 Hom.: 4682

Bravo AF: 0.438

Asia WGS AF: 0.505 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.9
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163075; hg19: chr10-105021263;