rs2066323

Positions:

• chr10-103111604-A-G

Variant summary

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

The NM_001351169.2(NT5C2):​c.176-4898T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.411 in 489,176 control chromosomes in the GnomAD database, including 41,923 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 (12973 hom., cov: 31)
  • Exomes 𝑓: 0.41 (28950 hom.)
• Consequence: NT5C2 NM_001351169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.71

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=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C2	NM_001351169.2	c.176-4898T>C		intron_variant		ENST00000404739.8	NP_001338098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000404739.8	c.176-4898T>C		intron_variant		1	NM_001351169.2	ENSP00000383960	P1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 62224 AN: 151818 Hom.: 12955 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.420

GnomAD4 exome AF: 0.411 AC: 138557 AN: 337240 Hom.: 28950 AF XY: 0.410 AC XY: 69121 AN XY: 168496

Gnomad4 AFR exome AF: 0.393

Gnomad4 AMR exome AF: 0.428

Gnomad4 ASJ exome AF: 0.428

Gnomad4 EAS exome AF: 0.467

Gnomad4 SAS exome AF: 0.454

Gnomad4 FIN exome AF: 0.370

Gnomad4 NFE exome AF: 0.407

Gnomad4 OTH exome AF: 0.421

GnomAD4 genome AF: 0.410 AC: 62287 AN: 151936 Hom.: 12973 Cov.: 31 AF XY: 0.408 AC XY: 30324 AN XY: 74250

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.558

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.423

Alfa AF: 0.414 Hom.: 2194

Bravo AF: 0.412

Asia WGS AF: 0.469 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	17
DANN	Benign	0.54

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: rs2066323; hg19: chr10-104871361;