rs7913461

Variant names:

• chr10-103241568-G-A
• rs7913461
• ENST00000674696.1:c.-25+34648C>T

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-25+34648C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 151,984 control chromosomes in the GnomAD database, including 30,461 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 0.62 (30461 hom., cov: 31)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0330

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.785 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000674696.1	c.-25+34648C>T		intron_variant	Intron 1 of 17			ENSP00000502679.1
NT5C2	ENST00000675326.1	c.-169+35586C>T		intron_variant	Intron 1 of 18			ENSP00000502205.1
NT5C2	ENST00000676428.1	c.-118+35586C>T		intron_variant	Intron 1 of 18			ENSP00000501689.1

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94606 AN: 151866 Hom.: 30415 Cov.: 31

Gnomad AFR AF: 0.793

Gnomad AMI AF: 0.683

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.437

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.623 AC: 94701 AN: 151984 Hom.: 30461 Cov.: 31 AF XY: 0.617 AC XY: 45825 AN XY: 74268

Gnomad4 AFR AF: 0.793

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.437

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.605

Alfa AF: 0.605 Hom.: 5443

Bravo AF: 0.639

Asia WGS AF: 0.531 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.62
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7913461; hg19: chr10-105001325;