10-103150133-A-G

Position:

• chr10-103150133-A-G

Variant summary

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

The NM_001351169.2(NT5C2):​c.102-10654T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.849 in 152,126 control chromosomes in the GnomAD database, including 55,248 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 0.85 (55248 hom., cov: 31)
• Consequence: NT5C2 NM_001351169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.905

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]

NT5C2 (HGNC:):

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 = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NT5C2	NM_001351169.2	c.102-10654T>C		intron_variant		ENST00000404739.8	NP_001338098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000404739.8	c.102-10654T>C		intron_variant		1	NM_001351169.2	ENSP00000383960.3

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128968 AN: 152008 Hom.: 55186 Cov.: 31

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.837

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.849

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

GnomAD4 genome AF: 0.849 AC: 129091 AN: 152126 Hom.: 55248 Cov.: 31 AF XY: 0.843 AC XY: 62716 AN XY: 74356

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.837

Gnomad4 EAS AF: 0.888

Gnomad4 SAS AF: 0.766

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.850

Alfa AF: 0.810 Hom.: 24905

Bravo AF: 0.869

Asia WGS AF: 0.815 AC: 2836 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.25
DANN	Benign	0.49

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1163249; hg19: chr10-104909890;