rs1891293

chr10-103242040-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+34176C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 151,798 control chromosomes in the GnomAD database, including 21,407 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 0.53 (21407 hom., cov: 30)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.551 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+34176C>T		intron_variant				P1
NT5C2	ENST00000675326.1	c.-169+35114C>T		intron_variant				P1
NT5C2	ENST00000676428.1	c.-118+35114C>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.529 AC: 80206 AN: 151680 Hom.: 21381 Cov.: 30

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.529 AC: 80282 AN: 151798 Hom.: 21407 Cov.: 30 AF XY: 0.526 AC XY: 38979 AN XY: 74156

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.523

Gnomad4 NFE AF: 0.555

Gnomad4 OTH AF: 0.537

Alfa AF: 0.544 Hom.: 3808

Bravo AF: 0.535

Asia WGS AF: 0.454 AC: 1580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	2.8
Dann	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1891293; hg19: chr10-105001797;