Genetic Variant UGT2B25P:n.69391612A>G (chr4-69391612-A-G) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PVS1_ModerateBA1

The ENST00000511504.2(UGT2B25P):n.868+1A>G variant causes a splice donor, intron change. The variant allele was found at a frequency of 0.156 in 1,385,200 control chromosomes in the GnomAD database, including 28,290 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: 𝑓 0.17 ( 2197 hom., cov: 29)

Exomes 𝑓: 0.16 ( 26093 hom. )

Consequence

UGT2B25P
ENST00000511504.2 splice_donor, intron

Scores

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 5.53

Variant links:

Genes affected

UGT2B25P (HGNC:12549): (UDP glucuronosyltransferase family 2 member B25, pseudogene)

UGT2B25P links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

PVS1

Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UGT2B25P		n.69391612A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UGT2B25P	ENST00000511504.2 link	n.868+1A>G		splice_donor_variant, intron_variant	Intron 2 of 5	6

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

24367

AN:

146486

Hom.:

2193

Cov.:

show subpopulations

Gnomad AFR

AF:

0.161

Gnomad AMI

AF:

0.185

Gnomad AMR

AF:

0.122

Gnomad ASJ

AF:

0.109

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.156

Gnomad FIN

AF:

0.166

Gnomad MID

AF:

0.0909

Gnomad NFE

AF:

0.189

Gnomad OTH

AF:

0.127

GnomAD4 exome

AF:

0.155

AC:

192217

AN:

1238606

Hom.:

26093

Cov.:

AF XY:

0.157

AC XY:

97405

AN XY:

618826

show subpopulations

Gnomad4 AFR exome

AF:

0.140

Gnomad4 AMR exome

AF:

0.101

Gnomad4 ASJ exome

AF:

0.100

Gnomad4 EAS exome

AF:

0.0991

Gnomad4 SAS exome

AF:

0.159

Gnomad4 FIN exome

AF:

0.184

Gnomad4 NFE exome

AF:

0.159

Gnomad4 OTH exome

AF:

0.148

GnomAD4 genome

AF:

0.166

AC:

24386

AN:

146594

Hom.:

2197

Cov.:

AF XY:

0.163

AC XY:

11621

AN XY:

71486

show subpopulations

Gnomad4 AFR

AF:

0.161

Gnomad4 AMR

AF:

0.122

Gnomad4 ASJ

AF:

0.109

Gnomad4 EAS

AF:

0.116

Gnomad4 SAS

AF:

0.155

Gnomad4 FIN

AF:

0.166

Gnomad4 NFE

AF:

0.189

Gnomad4 OTH

AF:

0.126

Alfa

AF:

0.0731

Hom.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Keratoconus

Uncertain:1

Apr 01, 2023

Institute of Human Genetics, Polish Academy of Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

DANN

Benign

0.85

Splicing

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