dbSNP rs3736922: NT5C2:c.1272+61C>T (chr10-103090875-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

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

The NM_001351169.2(NT5C2):c.1272+61C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 1,595,100 control chromosomes in the GnomAD database, including 145,056 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.43 ( 13997 hom., cov: 32)

Exomes 𝑓: 0.42 ( 131059 hom. )

Consequence

NT5C2
NM_001351169.2 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0450

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=-0.59).

BP6

Variant 10-103090875-G-A is Benign according to our data. Variant chr10-103090875-G-A is described in ClinVar as [Benign]. Clinvar id is 1295358.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NT5C2	NM_001351169.2 link	c.1272+61C>T		intron_variant	Intron 17 of 18	ENST00000404739.8	NP_001338098.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NT5C2	ENST00000404739.8 link	c.1272+61C>T		intron_variant	Intron 17 of 18	1	NM_001351169.2	ENSP00000383960.3		P49902-1

Frequencies

GnomAD3 genomes

AF:

0.426

AC:

64676

AN:

151862

Hom.:

13986

Cov.:

show subpopulations

Gnomad AFR

AF:

0.394

Gnomad AMI

AF:

0.388

Gnomad AMR

AF:

0.424

Gnomad ASJ

AF:

0.479

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.457

Gnomad FIN

AF:

0.380

Gnomad MID

AF:

0.478

Gnomad NFE

AF:

0.438

Gnomad OTH

AF:

0.437

GnomAD4 exome

AF:

0.424

AC:

612403

AN:

1443120

Hom.:

131059

Cov.:

AF XY:

0.426

AC XY:

306202

AN XY:

718820

show subpopulations

Gnomad4 AFR exome

AF:

0.391

Gnomad4 AMR exome

AF:

0.431

Gnomad4 ASJ exome

AF:

0.466

Gnomad4 EAS exome

AF:

0.502

Gnomad4 SAS exome

AF:

0.466

Gnomad4 FIN exome

AF:

0.381

Gnomad4 NFE exome

AF:

0.419

Gnomad4 OTH exome

AF:

0.436

GnomAD4 genome

AF:

0.426

AC:

64728

AN:

151980

Hom.:

13997

Cov.:

AF XY:

0.424

AC XY:

31500

AN XY:

74286

show subpopulations

Gnomad4 AFR

AF:

0.394

Gnomad4 AMR

AF:

0.424

Gnomad4 ASJ

AF:

0.479

Gnomad4 EAS

AF:

0.560

Gnomad4 SAS

AF:

0.457

Gnomad4 FIN

AF:

0.380

Gnomad4 NFE

AF:

0.438

Gnomad4 OTH

AF:

0.440

Alfa

AF:

0.431

Hom.:

3883

Bravo

AF:

0.428

Asia WGS

AF:

0.473

AC:

1642

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

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 26, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.59

CADD

Benign

4.0

DANN

Benign

0.51

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