Variant chr4-68816218-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001075.6(UGT2B10):c.199G>T(p.Asp67Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0851 in 1,613,000 control chromosomes in the GnomAD database, including 6,576 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.068 ( 388 hom., cov: 32)

Exomes 𝑓: 0.087 ( 6188 hom. )

Consequence

UGT2B10
NM_001075.6 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.420

Variant links:

Genes affected

UGT2B10 (HGNC:12544): (UDP glucuronosyltransferase family 2 member B10) Predicted to be involved in lipid metabolic process. Predicted to be located in endoplasmic reticulum membrane. Predicted to be integral component of membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

UGT2B10 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0018773675).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UGT2B10	NM_001075.6 linkuse as main transcript	c.199G>T	p.Asp67Tyr	missense_variant	1/6	ENST00000265403.12	NP_001066.1	P36537-1
UGT2B10	NM_001144767.3 linkuse as main transcript	c.199G>T	p.Asp67Tyr	missense_variant	1/6		NP_001138239.1	P36537-2
UGT2B10	XM_017008585.3 linkuse as main transcript	c.199G>T	p.Asp67Tyr	missense_variant	1/6		XP_016864074.1
UGT2B10	NM_001290091.2 linkuse as main transcript	c.-27+46G>T		intron_variant			NP_001277020.1	P36537

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT2B10	ENST00000265403.12 linkuse as main transcript	c.199G>T	p.Asp67Tyr	missense_variant	1/6	1	NM_001075.6	ENSP00000265403.7		P36537-1
UGT2B10	ENST00000458688.2 linkuse as main transcript	c.199G>T	p.Asp67Tyr	missense_variant	1/6	2		ENSP00000413420.2		P36537-2

Frequencies

GnomAD3 genomes

AF:

0.0683

AC:

10356

AN:

151680

Hom.:

388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0442

Gnomad AMI

AF:

0.0735

Gnomad AMR

AF:

0.0647

Gnomad ASJ

AF:

0.0652

Gnomad EAS

AF:

0.00250

Gnomad SAS

AF:

0.0350

Gnomad FIN

AF:

0.0586

Gnomad MID

AF:

0.0350

Gnomad NFE

AF:

0.0928

Gnomad OTH

AF:

0.0729

GnomAD3 exomes

AF:

0.0649

AC:

16261

AN:

250552

Hom.:

672

AF XY:

0.0663

AC XY:

8979

AN XY:

135506

show subpopulations

Gnomad AFR exome

AF:

0.0442

Gnomad AMR exome

AF:

0.0454

Gnomad ASJ exome

AF:

0.0779

Gnomad EAS exome

AF:

0.000710

Gnomad SAS exome

AF:

0.0391

Gnomad FIN exome

AF:

0.0571

Gnomad NFE exome

AF:

0.0911

Gnomad OTH exome

AF:

0.0711

GnomAD4 exome

AF:

0.0868

AC:

126842

AN:

1461202

Hom.:

6188

Cov.:

AF XY:

0.0855

AC XY:

62120

AN XY:

726924

show subpopulations

Gnomad4 AFR exome

AF:

0.0386

Gnomad4 AMR exome

AF:

0.0486

Gnomad4 ASJ exome

AF:

0.0777

Gnomad4 EAS exome

AF:

0.000530

Gnomad4 SAS exome

AF:

0.0414

Gnomad4 FIN exome

AF:

0.0600

Gnomad4 NFE exome

AF:

0.0987

Gnomad4 OTH exome

AF:

0.0772

GnomAD4 genome

AF:

0.0682

AC:

10360

AN:

151798

Hom.:

388

Cov.:

AF XY:

0.0661

AC XY:

4907

AN XY:

74200

show subpopulations

Gnomad4 AFR

AF:

0.0442

Gnomad4 AMR

AF:

0.0646

Gnomad4 ASJ

AF:

0.0652

Gnomad4 EAS

AF:

0.00251

Gnomad4 SAS

AF:

0.0351

Gnomad4 FIN

AF:

0.0586

Gnomad4 NFE

AF:

0.0928

Gnomad4 OTH

AF:

0.0722

Alfa

AF:

0.0637

Hom.:

125

Bravo

AF:

0.0686

TwinsUK

AF:

0.113

AC:

418

ALSPAC

AF:

0.0968

AC:

373

ESP6500AA

AF:

0.0418

AC:

184

ESP6500EA

AF:

0.0917

AC:

788

ExAC

AF:

0.0653

AC:

7927

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.0851

EpiControl

AF:

0.0909

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.095

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.66

CADD

Benign

5.2

DANN

Benign

0.37

DEOGEN2

Benign

0.0095

T;.

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.8

FATHMM_MKL

Benign

0.26

LIST_S2

Benign

0.066

T;T

MetaRNN

Benign

0.0019

T;T

MetaSVM

Benign

-1.0

MutationAssessor

Benign

0.42

N;N

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.29

PROVEAN

Benign

-1.6

N;N

REVEL

Benign

0.051

Sift

Uncertain

0.019

D;D

Sift4G

Uncertain

0.047

D;T

Polyphen

0.012

B;.

Vest4

0.073

MPC

0.024

ClinPred

0.041

GERP RS

-4.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.021

gMVP

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over