Variant rs11191553 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.1160-24C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 1,597,430 control chromosomes in the GnomAD database, including 75,451 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 7526 hom., cov: 33)

Exomes 𝑓: 0.30 ( 67925 hom. )

Consequence

NT5C2
NM_001351169.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.557

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=-0.66).

BP6

Variant 10-103091639-G-T is Benign according to our data. Variant chr10-103091639-G-T is described in ClinVar as [Benign]. Clinvar id is 667744.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 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.1160-24C>A		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.1160-24C>A		intron_variant		1	NM_001351169.2	ENSP00000383960	P1	P49902-1

Frequencies

GnomAD3 genomes

AF:

0.312

AC:

47383

AN:

151966

Hom.:

7520

Cov.:

show subpopulations

Gnomad AFR

AF:

0.328

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.265

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.208

Gnomad SAS

AF:

0.245

Gnomad FIN

AF:

0.290

Gnomad MID

AF:

0.360

Gnomad NFE

AF:

0.325

Gnomad OTH

AF:

0.314

GnomAD3 exomes

AF:

0.286

AC:

71529

AN:

250322

Hom.:

10616

AF XY:

0.287

AC XY:

38864

AN XY:

135324

show subpopulations

Gnomad AFR exome

AF:

0.327

Gnomad AMR exome

AF:

0.206

Gnomad ASJ exome

AF:

0.348

Gnomad EAS exome

AF:

0.211

Gnomad SAS exome

AF:

0.241

Gnomad FIN exome

AF:

0.289

Gnomad NFE exome

AF:

0.321

Gnomad OTH exome

AF:

0.304

GnomAD4 exome

AF:

0.302

AC:

436583

AN:

1445346

Hom.:

67925

Cov.:

AF XY:

0.301

AC XY:

216570

AN XY:

719950

show subpopulations

Gnomad4 AFR exome

AF:

0.332

Gnomad4 AMR exome

AF:

0.214

Gnomad4 ASJ exome

AF:

0.345

Gnomad4 EAS exome

AF:

0.159

Gnomad4 SAS exome

AF:

0.241

Gnomad4 FIN exome

AF:

0.288

Gnomad4 NFE exome

AF:

0.314

Gnomad4 OTH exome

AF:

0.306

GnomAD4 genome

AF:

0.312

AC:

47414

AN:

152084

Hom.:

7526

Cov.:

AF XY:

0.307

AC XY:

22857

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.328

Gnomad4 AMR

AF:

0.264

Gnomad4 ASJ

AF:

0.362

Gnomad4 EAS

AF:

0.207

Gnomad4 SAS

AF:

0.245

Gnomad4 FIN

AF:

0.290

Gnomad4 NFE

AF:

0.325

Gnomad4 OTH

AF:

0.314

Alfa

AF:

0.320

Hom.:

7861

Bravo

AF:

0.310

Asia WGS

AF:

0.227

AC:

788

AN:

3478

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	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. -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.66

CADD

Benign

DANN

Benign

0.80

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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