Variant rs3756669 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_152404.4(UGT3A1):c.361T>G(p.Cys121Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 1,599,150 control chromosomes in the GnomAD database, including 23,002 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.13 ( 1890 hom., cov: 33)

Exomes 𝑓: 0.16 ( 21112 hom. )

Consequence

UGT3A1
NM_152404.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.52

Variant links:

Genes affected

UGT3A1 (HGNC:26625): (UDP glycosyltransferase family 3 member A1) Enables glucuronosyltransferase activity. Part of UDP-N-acetylglucosamine transferase complex. [provided by Alliance of Genome Resources, Apr 2022]

UGT3A1 links:

UGT3A1 (HGNC:):

UGT3A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGT3A1	NM_152404.4 linkuse as main transcript	c.361T>G	p.Cys121Gly	missense_variant	4/7	ENST00000274278.8	NP_689617.3	Q6NUS8-1A8K444B7Z3N0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT3A1	ENST00000274278.8 linkuse as main transcript	c.361T>G	p.Cys121Gly	missense_variant	4/7	1	NM_152404.4	ENSP00000274278.3		Q6NUS8-1

Frequencies

GnomAD3 genomes

AF:

0.131

AC:

19971

AN:

152142

Hom.:

1887

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0370

Gnomad AMI

AF:

0.0582

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.137

Gnomad EAS

AF:

0.379

Gnomad SAS

AF:

0.342

Gnomad FIN

AF:

0.129

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.144

Gnomad OTH

AF:

0.138

GnomAD3 exomes

AF:

0.191

AC:

45214

AN:

236240

Hom.:

5621

AF XY:

0.197

AC XY:

25303

AN XY:

128400

show subpopulations

Gnomad AFR exome

AF:

0.0347

Gnomad AMR exome

AF:

0.238

Gnomad ASJ exome

AF:

0.146

Gnomad EAS exome

AF:

0.406

Gnomad SAS exome

AF:

0.338

Gnomad FIN exome

AF:

0.124

Gnomad NFE exome

AF:

0.145

Gnomad OTH exome

AF:

0.164

GnomAD4 exome

AF:

0.159

AC:

229392

AN:

1446890

Hom.:

21112

Cov.:

AF XY:

0.164

AC XY:

117462

AN XY:

718410

show subpopulations

Gnomad4 AFR exome

AF:

0.0339

Gnomad4 AMR exome

AF:

0.233

Gnomad4 ASJ exome

AF:

0.142

Gnomad4 EAS exome

AF:

0.332

Gnomad4 SAS exome

AF:

0.333

Gnomad4 FIN exome

AF:

0.127

Gnomad4 NFE exome

AF:

0.141

Gnomad4 OTH exome

AF:

0.171

GnomAD4 genome

AF:

0.131

AC:

19986

AN:

152260

Hom.:

1890

Cov.:

AF XY:

0.135

AC XY:

10080

AN XY:

74446

show subpopulations

Gnomad4 AFR

AF:

0.0369

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.137

Gnomad4 EAS

AF:

0.379

Gnomad4 SAS

AF:

0.343

Gnomad4 FIN

AF:

0.129

Gnomad4 NFE

AF:

0.144

Gnomad4 OTH

AF:

0.141

Alfa

AF:

0.151

Hom.:

4302

Bravo

AF:

0.127

TwinsUK

AF:

0.141

AC:

522

ALSPAC

AF:

0.145

AC:

557

ESP6500AA

AF:

0.0356

AC:

157

ESP6500EA

AF:

0.140

AC:

1201

ExAC

AF:

0.187

AC:

22638

Asia WGS

AF:

0.322

AC:

1121

AN:

3478

EpiCase

AF:

0.148

EpiControl

AF:

0.142

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.79

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.18

CADD

Benign

DANN

Benign

0.97

DEOGEN2

Benign

0.098

T;.;.;.;.

Eigen

Benign

0.13

Eigen_PC

Benign

-0.15

FATHMM_MKL

Benign

0.18

LIST_S2

Benign

0.69

T;T;T;.;T

MetaRNN

Benign

0.0048

T;T;T;T;T

MetaSVM

Benign

-1.2

MutationAssessor

Pathogenic

3.3

M;.;.;.;.

PrimateAI

Uncertain

0.49

PROVEAN

Pathogenic

-9.3

D;D;D;.;D

REVEL

Uncertain

0.40

Sift

Pathogenic

0.0

D;D;D;.;D

Sift4G

Pathogenic

0.0

D;D;D;D;D

Polyphen

1.0

D;D;D;.;.

Vest4

0.38

MPC

0.21

ClinPred

0.11

GERP RS

3.0

Varity_R

0.91

gMVP

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.24

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.24

Position offset: 0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over