chr10-103203294-G-C

Variant names:

• chr10-103203294-G-C
• rs4917999
• ENST00000674696.1:c.-24-28312C>G

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-24-28312C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.286 in 151,298 control chromosomes in the GnomAD database, including 6,387 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 0.29 (6387 hom., cov: 30)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.890

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.304 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.-24-28312C>G		intron_variant	Intron 1 of 17			ENSP00000502679.1
NT5C2	ENST00000675326.1	c.-168-21966C>G		intron_variant	Intron 1 of 18			ENSP00000502205.1
NT5C2	ENST00000676428.1	c.-117-5437C>G		intron_variant	Intron 1 of 18			ENSP00000501689.1

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43196 AN: 151182 Hom.: 6382 Cov.: 30

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.252

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.307

Gnomad OTH AF: 0.288

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

GnomAD4 genome AF: 0.286 AC: 43230 AN: 151298 Hom.: 6387 Cov.: 30 AF XY: 0.281 AC XY: 20717 AN XY: 73838

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.315

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.124

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.307

Gnomad4 OTH AF: 0.287

Alfa AF: 0.182 Hom.: 395

Bravo AF: 0.285

Asia WGS AF: 0.137 AC: 476 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.8
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4917999; hg19: chr10-104963051;