rs7095304

Variant names:

• chr10-103195038-G-A
• rs7095304
• ENST00000674696.1:c.-24-20056C>T

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000674696.1	c.-24-20056C>T		intron_variant	Intron 1 of 17			ENSP00000502679.1
NT5C2	ENST00000675326.1	c.-168-13710C>T		intron_variant	Intron 1 of 18			ENSP00000502205.1
NT5C2	ENST00000676428.1	c.-25+2727C>T		intron_variant	Intron 2 of 18			ENSP00000501689.1

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;