rs1163073

chr10-103263177-T-Cchr10-103263177-T-G

Variant summary

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

The ENST00000674696.1(NT5C2):c.-25+13039A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,950 control chromosomes in the GnomAD database, including 6,667 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 0.27 (6667 hom., cov: 32)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.127

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=-0.5).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.477 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+13039A>G		intron_variant				P1
NT5C2	ENST00000675326.1	c.-169+13977A>G		intron_variant				P1
NT5C2	ENST00000676428.1	c.-118+13977A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.267 AC: 40508 AN: 151832 Hom.: 6663 Cov.: 32

Gnomad AFR AF: 0.0723

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.330

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.267 AC: 40510 AN: 151950 Hom.: 6667 Cov.: 32 AF XY: 0.274 AC XY: 20382 AN XY: 74270

Gnomad4 AFR AF: 0.0721

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.391

Gnomad4 SAS AF: 0.494

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.330

Gnomad4 OTH AF: 0.277

Alfa AF: 0.293 Hom.: 3792

Bravo AF: 0.244

Asia WGS AF: 0.413 AC: 1431 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
Cadd	Benign	12
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163073; hg19: chr10-105022934;