10-103243964-T-G

Variant names:

• chr10-103243964-T-G
• rs4917385
• ENST00000674696.1:c.-25+32252A>C

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-25+32252A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 151,758 control chromosomes in the GnomAD database, including 42,115 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 0.73 (42115 hom., cov: 29)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.92 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+32252A>C		intron_variant	Intron 1 of 17			ENSP00000502679.1
NT5C2	ENST00000675326.1	c.-169+33190A>C		intron_variant	Intron 1 of 18			ENSP00000502205.1
NT5C2	ENST00000676428.1	c.-118+33190A>C		intron_variant	Intron 1 of 18			ENSP00000501689.1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111209 AN: 151640 Hom.: 42054 Cov.: 29

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.812

Gnomad AMR AF: 0.706

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.722

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

GnomAD4 genome AF: 0.734 AC: 111324 AN: 151758 Hom.: 42115 Cov.: 29 AF XY: 0.726 AC XY: 53805 AN XY: 74138

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.595

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.722

Alfa AF: 0.714 Hom.: 4912

Bravo AF: 0.756

Asia WGS AF: 0.583 AC: 2033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	7.8
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4917385; hg19: chr10-105003721;