chr10-103195038-G-A

Position:

• chr10-103195038-G-A

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-24-20056C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.311 in 151,892 control chromosomes in the GnomAD database, including 7,469 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 0.31 (7469 hom., cov: 32)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.675

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 (AFR) allele frequency at 95% confidence interval = 0.324 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000674696.1	c.-24-20056C>T		intron_variant				ENSP00000502679	P1
NT5C2	ENST00000675326.1	c.-168-13710C>T		intron_variant				ENSP00000502205	P1
NT5C2	ENST00000676428.1	c.-25+2727C>T		intron_variant				ENSP00000501689	P1

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47163 AN: 151774 Hom.: 7463 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.312

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

GnomAD4 genome AF: 0.311 AC: 47194 AN: 151892 Hom.: 7469 Cov.: 32 AF XY: 0.306 AC XY: 22742 AN XY: 74218

Gnomad4 AFR AF: 0.328

Gnomad4 AMR AF: 0.263

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.311

Alfa AF: 0.318 Hom.: 7196

Bravo AF: 0.309

Asia WGS AF: 0.224 AC: 779 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	9.3
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7095304; hg19: chr10-104954795;