rs1163238

chr10-103184236-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.-168-2908C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,024 control chromosomes in the GnomAD database, including 13,405 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 0.41 (13405 hom., cov: 32)
• Consequence: NT5C2 NM_001351169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NT5C2	NM_001351169.2	c.-168-2908C>T		intron_variant		ENST00000404739.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C2	ENST00000404739.8	c.-168-2908C>T		intron_variant		1	NM_001351169.2	P1

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61877 AN: 151906 Hom.: 13393 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.487

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.388

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

GnomAD4 genome AF: 0.407 AC: 61920 AN: 152024 Hom.: 13405 Cov.: 32 AF XY: 0.400 AC XY: 29715 AN XY: 74298

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.263

Gnomad4 FIN AF: 0.289

Gnomad4 NFE AF: 0.370

Gnomad4 OTH AF: 0.386

Alfa AF: 0.385 Hom.: 1492

Bravo AF: 0.417

Asia WGS AF: 0.266 AC: 928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	1.1
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163238; hg19: chr10-104943993;