Variant chr10-103095913-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001351169.2(NT5C2):c.813+26C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 1,577,372 control chromosomes in the GnomAD database, including 73,626 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7538 hom., cov: 31)

Exomes 𝑓: 0.30 ( 66088 hom. )

Consequence

NT5C2
NM_001351169.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.583

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 10-103095913-G-A is Benign according to our data. Variant chr10-103095913-G-A is described in ClinVar as [Benign]. Clinvar id is 667734.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

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
NT5C2	NM_001351169.2 linkuse as main transcript	c.813+26C>T		intron_variant		ENST00000404739.8	NP_001338098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000404739.8 linkuse as main transcript	c.813+26C>T		intron_variant		1	NM_001351169.2	ENSP00000383960	P1	P49902-1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47405

AN:

151818

Hom.:

7533

Cov.:

show subpopulations

Gnomad AFR

AF:

0.329

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.365

Gnomad EAS

AF:

0.209

Gnomad SAS

AF:

0.244

Gnomad FIN

AF:

0.291

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.326

Gnomad OTH

AF:

0.315

GnomAD3 exomes

AF:

0.286

AC:

71564

AN:

249880

Hom.:

10628

AF XY:

0.288

AC XY:

38850

AN XY:

135034

show subpopulations

Gnomad AFR exome

AF:

0.327

Gnomad AMR exome

AF:

0.207

Gnomad ASJ exome

AF:

0.352

Gnomad EAS exome

AF:

0.214

Gnomad SAS exome

AF:

0.241

Gnomad FIN exome

AF:

0.289

Gnomad NFE exome

AF:

0.321

Gnomad OTH exome

AF:

0.305

GnomAD4 exome

AF:

0.300

AC:

427314

AN:

1425436

Hom.:

66088

Cov.:

AF XY:

0.299

AC XY:

212607

AN XY:

711314

show subpopulations

Gnomad4 AFR exome

AF:

0.331

Gnomad4 AMR exome

AF:

0.215

Gnomad4 ASJ exome

AF:

0.348

Gnomad4 EAS exome

AF:

0.160

Gnomad4 SAS exome

AF:

0.240

Gnomad4 FIN exome

AF:

0.289

Gnomad4 NFE exome

AF:

0.311

Gnomad4 OTH exome

AF:

0.305

GnomAD4 genome

AF:

0.312

AC:

47435

AN:

151936

Hom.:

7538

Cov.:

AF XY:

0.308

AC XY:

22863

AN XY:

74254

show subpopulations

Gnomad4 AFR

AF:

0.329

Gnomad4 AMR

AF:

0.264

Gnomad4 ASJ

AF:

0.365

Gnomad4 EAS

AF:

0.208

Gnomad4 SAS

AF:

0.244

Gnomad4 FIN

AF:

0.291

Gnomad4 NFE

AF:

0.326

Gnomad4 OTH

AF:

0.315

Alfa

AF:

0.324

Hom.:

2155

Bravo

AF:

0.310

Asia WGS

AF:

0.224

AC:

779

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

2.2

DANN

Benign

0.63

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over