Variant rs3219235 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_080911.3(UNG):c.534-25dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 1,548,134 control chromosomes in the GnomAD database, including 29,381 homozygotes. Variant has been reported in ClinVar as Benign (★★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.19 ( 2748 hom., cov: 27)

Exomes 𝑓: 0.19 ( 26633 hom. )

Consequence

UNG
NM_080911.3 intron

Scores

Not classified

Clinical Significance

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

Conservation

PhyloP100: -1.40

Variant links:

Genes affected

UNG (HGNC:12572): (uracil DNA glycosylase) This gene encodes one of several uracil-DNA glycosylases. One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosylic bond and initiating the base-excision repair (BER) pathway. Uracil bases occur from cytosine deamination or misincorporation of dUMP residues. Alternative promoter usage and splicing of this gene leads to two different isoforms: the mitochondrial UNG1 and the nuclear UNG2. The UNG2 term was used as a previous symbol for the CCNO gene (GeneID 10309), which has been confused with this gene, in the literature and some databases. [provided by RefSeq, Nov 2010]

UNG links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 12-109102808-G-GT is Benign according to our data. Variant chr12-109102808-G-GT is described in ClinVar as [Benign]. Clinvar id is 1249431.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UNG	NM_080911.3 linkuse as main transcript	c.534-25dup		intron_variant		ENST00000242576.7
UNG	NM_003362.4 linkuse as main transcript	c.507-25dup		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UNG	ENST00000242576.7 linkuse as main transcript	c.534-25dup		intron_variant		1	NM_080911.3	P1	P13051-1

Frequencies

GnomAD3 genomes

AF:

0.190

AC:

28859

AN:

151846

Hom.:

2746

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.138

Gnomad AMR

AF:

0.180

Gnomad ASJ

AF:

0.246

Gnomad EAS

AF:

0.323

Gnomad SAS

AF:

0.272

Gnomad FIN

AF:

0.201

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.185

Gnomad OTH

AF:

0.177

GnomAD3 exomes

AF:

0.208

AC:

52010

AN:

250470

Hom.:

5828

AF XY:

0.211

AC XY:

28586

AN XY:

135528

show subpopulations

Gnomad AFR exome

AF:

0.176

Gnomad AMR exome

AF:

0.165

Gnomad ASJ exome

AF:

0.242

Gnomad EAS exome

AF:

0.340

Gnomad SAS exome

AF:

0.274

Gnomad FIN exome

AF:

0.198

Gnomad NFE exome

AF:

0.186

Gnomad OTH exome

AF:

0.192

GnomAD4 exome

AF:

0.190

AC:

265847

AN:

1396170

Hom.:

26633

Cov.:

AF XY:

0.193

AC XY:

134777

AN XY:

698908

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.163

Gnomad4 ASJ exome

AF:

0.239

Gnomad4 EAS exome

AF:

0.312

Gnomad4 SAS exome

AF:

0.266

Gnomad4 FIN exome

AF:

0.197

Gnomad4 NFE exome

AF:

0.180

Gnomad4 OTH exome

AF:

0.195

GnomAD4 genome

AF:

0.190

AC:

28864

AN:

151964

Hom.:

2748

Cov.:

AF XY:

0.193

AC XY:

14311

AN XY:

74242

show subpopulations

Gnomad4 AFR

AF:

0.171

Gnomad4 AMR

AF:

0.180

Gnomad4 ASJ

AF:

0.246

Gnomad4 EAS

AF:

0.323

Gnomad4 SAS

AF:

0.272

Gnomad4 FIN

AF:

0.201

Gnomad4 NFE

AF:

0.185

Gnomad4 OTH

AF:

0.179

Alfa

AF:

0.189

Hom.:

501

Bravo

AF:

0.184

Asia WGS

AF:

0.267

AC:

929

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 35% of patients studied by a panel of primary immunodeficiencies. Number of patients: 33. Only high quality variants are reported. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 03, 2015

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BranchPoint Hunter

2.0

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