Variant chr10-103095899-T-C 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+40A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 1,532,738 control chromosomes in the GnomAD database, including 123,736 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.41 ( 13016 hom., cov: 31)

Exomes 𝑓: 0.40 ( 110720 hom. )

Consequence

NT5C2
NM_001351169.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.104

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=-0.88).

BP6

Variant 10-103095899-T-C is Benign according to our data. Variant chr10-103095899-T-C is described in ClinVar as [Benign]. Clinvar id is 1235346.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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+40A>G		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+40A>G		intron_variant		1	NM_001351169.2	ENSP00000383960.3		P49902-1

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

62358

AN:

151846

Hom.:

13003

Cov.:

show subpopulations

Gnomad AFR

AF:

0.389

Gnomad AMI

AF:

0.350

Gnomad AMR

AF:

0.404

Gnomad ASJ

AF:

0.440

Gnomad EAS

AF:

0.558

Gnomad SAS

AF:

0.450

Gnomad FIN

AF:

0.368

Gnomad MID

AF:

0.434

Gnomad NFE

AF:

0.417

Gnomad OTH

AF:

0.421

GnomAD3 exomes

AF:

0.423

AC:

105460

AN:

249090

Hom.:

22592

AF XY:

0.425

AC XY:

57122

AN XY:

134528

show subpopulations

Gnomad AFR exome

AF:

0.386

Gnomad AMR exome

AF:

0.415

Gnomad ASJ exome

AF:

0.433

Gnomad EAS exome

AF:

0.564

Gnomad SAS exome

AF:

0.454

Gnomad FIN exome

AF:

0.374

Gnomad NFE exome

AF:

0.409

Gnomad OTH exome

AF:

0.420

GnomAD4 exome

AF:

0.397

AC:

548607

AN:

1380772

Hom.:

110720

Cov.:

AF XY:

0.400

AC XY:

276585

AN XY:

691476

show subpopulations

Gnomad4 AFR exome

AF:

0.380

Gnomad4 AMR exome

AF:

0.419

Gnomad4 ASJ exome

AF:

0.427

Gnomad4 EAS exome

AF:

0.501

Gnomad4 SAS exome

AF:

0.455

Gnomad4 FIN exome

AF:

0.373

Gnomad4 NFE exome

AF:

0.388

Gnomad4 OTH exome

AF:

0.408

GnomAD4 genome

AF:

0.411

AC:

62414

AN:

151966

Hom.:

13016

Cov.:

AF XY:

0.409

AC XY:

30381

AN XY:

74264

show subpopulations

Gnomad4 AFR

AF:

0.389

Gnomad4 AMR

AF:

0.404

Gnomad4 ASJ

AF:

0.440

Gnomad4 EAS

AF:

0.557

Gnomad4 SAS

AF:

0.450

Gnomad4 FIN

AF:

0.368

Gnomad4 NFE

AF:

0.417

Gnomad4 OTH

AF:

0.424

Alfa

AF:

0.416

Hom.:

12413

Bravo

AF:

0.412

Asia WGS

AF:

0.465

AC:

1614

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	clinical testing	GeneDx	Jun 26, 2018	- -
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

-0.88

CADD

Benign

2.0

DANN

Benign

0.43

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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