rs11191580

Positions:

• chr10-103146454-T-C

Variant summary

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

The ENST00000404739.8(NT5C2):​c.102-6975A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0803 in 984,390 control chromosomes in the GnomAD database, including 3,899 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 0.083 (819 hom., cov: 32)
  • Exomes 𝑓: 0.080 (3080 hom.)
• Consequence: NT5C2 ENST00000404739.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.558

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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C2	NM_001351169.2	c.102-6975A>G		intron_variant		ENST00000404739.8	NP_001338098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000404739.8	c.102-6975A>G		intron_variant		1	NM_001351169.2	ENSP00000383960	P1

Frequencies

GnomAD3 genomes AF: 0.0835 AC: 12700 AN: 152156 Hom.: 815 Cov.: 32

Gnomad AFR AF: 0.0213

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.0720

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.0746

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0903

Gnomad OTH AF: 0.0975

GnomAD4 exome AF: 0.0797 AC: 66304 AN: 832116 Hom.: 3080 Cov.: 26 AF XY: 0.0800 AC XY: 30739 AN XY: 384294

Gnomad4 AFR exome AF: 0.0107

Gnomad4 AMR exome AF: 0.179

Gnomad4 ASJ exome AF: 0.0747

Gnomad4 EAS exome AF: 0.275

Gnomad4 SAS exome AF: 0.208

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.0767

Gnomad4 OTH exome AF: 0.0968

GnomAD4 genome AF: 0.0835 AC: 12709 AN: 152274 Hom.: 819 Cov.: 32 AF XY: 0.0861 AC XY: 6408 AN XY: 74458

Gnomad4 AFR AF: 0.0212

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.0720

Gnomad4 EAS AF: 0.277

Gnomad4 SAS AF: 0.184

Gnomad4 FIN AF: 0.0746

Gnomad4 NFE AF: 0.0904

Gnomad4 OTH AF: 0.100

Alfa AF: 0.0970 Hom.: 1043

Bravo AF: 0.0855

Asia WGS AF: 0.193 AC: 670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	14
DANN	Benign	0.85

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: rs11191580; hg19: chr10-104906211;