rs4917384

Positions:

• chr10-103236031-T-C
• chr10-103236031-T-G

Variant summary

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

The ENST00000674696.1(NT5C2):​c.-25+40185A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 151,996 control chromosomes in the GnomAD database, including 42,592 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 0.74 (42592 hom., cov: 31)
• Consequence: NT5C2 ENST00000674696.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.19

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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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.-25+40185A>G		intron_variant				ENSP00000502679	P1
NT5C2	ENST00000675326.1	c.-169+41123A>G		intron_variant				ENSP00000502205	P1
NT5C2	ENST00000676428.1	c.-117-38174A>G		intron_variant				ENSP00000501689	P1

Frequencies

GnomAD3 genomes AF: 0.737 AC: 111970 AN: 151878 Hom.: 42530 Cov.: 31

Gnomad AFR AF: 0.928

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.710

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.597

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.737 AC: 112086 AN: 151996 Hom.: 42592 Cov.: 31 AF XY: 0.729 AC XY: 54173 AN XY: 74288

Gnomad4 AFR AF: 0.929

Gnomad4 AMR AF: 0.710

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.597

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.724

Alfa AF: 0.702 Hom.: 7460

Bravo AF: 0.760

Asia WGS AF: 0.583 AC: 2030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.61
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4917384; hg19: chr10-104995788;