10-103193790-T-C

Position:

• chr10-103193790-T-C

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-24-18808A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 151,954 control chromosomes in the GnomAD database, including 12,958 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 (12958 hom., cov: 31)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.31

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NT5C2	ENST00000674696.1	c.-24-18808A>G		intron_variant				P1
NT5C2	ENST00000675326.1	c.-168-12462A>G		intron_variant				P1
NT5C2	ENST00000676428.1	c.-25+3975A>G		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.409 AC: 62166 AN: 151838 Hom.: 12940 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.350

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.410 AC: 62228 AN: 151954 Hom.: 12958 Cov.: 31 AF XY: 0.408 AC XY: 30281 AN XY: 74244

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.437

Gnomad4 EAS AF: 0.559

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.423

Alfa AF: 0.428 Hom.: 2379

Bravo AF: 0.411

Asia WGS AF: 0.468 AC: 1625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.6
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10748839; hg19: chr10-104953547;