rs7913461

chr10-103241568-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+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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C2	ENST00000674696.1	c.-25+34648C>T		intron_variant				P1
NT5C2	ENST00000675326.1	c.-169+35586C>T		intron_variant				P1
NT5C2	ENST00000676428.1	c.-118+35586C>T		intron_variant				P1

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;