rs12261294

chr10-103175195-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001351169.2(NT5C2):c.-24-213G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,860 control chromosomes in the GnomAD database, including 1,781 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.15 (1781 hom., cov: 32)
• Consequence: NT5C2 NM_001351169.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.270

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 10-103175195-C-T is Benign according to our data. Variant chr10-103175195-C-T is described in ClinVar as [Benign]. Clinvar id is 1237245.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.162 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C2	NM_001351169.2	c.-24-213G>A		intron_variant		ENST00000404739.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C2	ENST00000404739.8	c.-24-213G>A		intron_variant		1	NM_001351169.2	P1

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22790 AN: 151742 Hom.: 1778 Cov.: 32

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0173

Gnomad SAS AF: 0.0828

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.150 AC: 22812 AN: 151860 Hom.: 1781 Cov.: 32 AF XY: 0.148 AC XY: 10985 AN XY: 74208

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0172

Gnomad4 SAS AF: 0.0837

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.152

Alfa AF: 0.160 Hom.: 248

Bravo AF: 0.153

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	6.4
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12261294; hg19: chr10-104934952;