chr10-103200095-C-A

Position:

• chr10-103200095-C-A

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-24-25113G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,042 control chromosomes in the GnomAD database, including 12,871 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 (12871 hom., cov: 32)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.285

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.513 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.-24-25113G>T		intron_variant				P1
NT5C2	ENST00000675326.1	c.-168-18767G>T		intron_variant				P1
NT5C2	ENST00000676428.1	c.-117-2238G>T		intron_variant				P1

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62022 AN: 151924 Hom.: 12853 Cov.: 32

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.402

Gnomad ASJ AF: 0.436

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.367

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: 0.408 AC: 62086 AN: 152042 Hom.: 12871 Cov.: 32 AF XY: 0.407 AC XY: 30217 AN XY: 74308

Gnomad4 AFR AF: 0.390

Gnomad4 AMR AF: 0.402

Gnomad4 ASJ AF: 0.436

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.422

Alfa AF: 0.384 Hom.: 5138

Bravo AF: 0.410

Asia WGS AF: 0.445 AC: 1544 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.62
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4307650; hg19: chr10-104959852;