rs11191582

chr10-103153896-G-A

Variant summary

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

The NM_001351169.2(NT5C2):c.102-14417C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0725 in 623,274 control chromosomes in the GnomAD database, including 2,295 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 0.082 (777 hom., cov: 32)
  • Exomes 𝑓: 0.069 (1518 hom.)
• Consequence: NT5C2 NM_001351169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

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 (EAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C2	NM_001351169.2	c.102-14417C>T		intron_variant		ENST00000404739.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C2	ENST00000404739.8	c.102-14417C>T		intron_variant		1	NM_001351169.2	P1

Frequencies

GnomAD3 genomes AF: 0.0820 AC: 12472 AN: 152088 Hom.: 773 Cov.: 32

Gnomad AFR AF: 0.0201

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0967

GnomAD4 exome AF: 0.0695 AC: 32719 AN: 471068 Hom.: 1518 AF XY: 0.0697 AC XY: 15413 AN XY: 221168

Gnomad4 AFR exome AF: 0.00862

Gnomad4 AMR exome AF: 0.159

Gnomad4 ASJ exome AF: 0.0662

Gnomad4 EAS exome AF: 0.234

Gnomad4 SAS exome AF: 0.188

Gnomad4 FIN exome AF: 0.0617

Gnomad4 NFE exome AF: 0.0670

Gnomad4 OTH exome AF: 0.0822

GnomAD4 genome AF: 0.0820 AC: 12482 AN: 152206 Hom.: 777 Cov.: 32 AF XY: 0.0845 AC XY: 6290 AN XY: 74416

Gnomad4 AFR AF: 0.0201

Gnomad4 AMR AF: 0.134

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.182

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0903

Gnomad4 OTH AF: 0.0995

Alfa AF: 0.0828 Hom.: 84

Bravo AF: 0.0838

Asia WGS AF: 0.173 AC: 600 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	6.7
Dann	Benign	0.52

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs11191582; hg19: chr10-104913653;