Variant rs11820589 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_032725.4(BUD13):c.443C>T(p.Pro148Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0719 in 1,599,516 control chromosomes in the GnomAD database, including 4,944 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 0.099 ( 945 hom., cov: 32)

Exomes 𝑓: 0.069 ( 3999 hom. )

Consequence

BUD13
NM_032725.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.04

Variant links:

Genes affected

BUD13 (HGNC:28199): (BUD13 homolog) Enables RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in nucleoplasm. Part of U2-type precatalytic spliceosome. [provided by Alliance of Genome Resources, Apr 2022]

BUD13 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017516613).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BUD13	NM_032725.4 linkuse as main transcript	c.443C>T	p.Pro148Leu	missense_variant	4/10	ENST00000260210.5	NP_116114.1	Q9BRD0-1
BUD13	NM_001159736.2 linkuse as main transcript	c.443C>T	p.Pro148Leu	missense_variant	4/10		NP_001153208.1	Q9BRD0-2
BUD13	XM_011543035.3 linkuse as main transcript	c.344C>T	p.Pro115Leu	missense_variant	4/10		XP_011541337.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BUD13	ENST00000260210.5 linkuse as main transcript	c.443C>T	p.Pro148Leu	missense_variant	4/10	1	NM_032725.4	ENSP00000260210.3		Q9BRD0-1
BUD13	ENST00000375445.7 linkuse as main transcript	c.443C>T	p.Pro148Leu	missense_variant	4/10	1		ENSP00000364594.3		Q9BRD0-2

Frequencies

GnomAD3 genomes

AF:

0.0987

AC:

14989

AN:

151892

Hom.:

941

Cov.:

show subpopulations

Gnomad AFR

AF:

0.171

Gnomad AMI

AF:

0.121

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.0709

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0456

Gnomad FIN

AF:

0.0603

Gnomad MID

AF:

0.0796

Gnomad NFE

AF:

0.0673

Gnomad OTH

AF:

0.104

GnomAD3 exomes

AF:

0.0784

AC:

19391

AN:

247394

Hom.:

1033

AF XY:

0.0724

AC XY:

9673

AN XY:

133576

show subpopulations

Gnomad AFR exome

AF:

0.168

Gnomad AMR exome

AF:

0.156

Gnomad ASJ exome

AF:

0.0703

Gnomad EAS exome

AF:

0.000326

Gnomad SAS exome

AF:

0.0414

Gnomad FIN exome

AF:

0.0660

Gnomad NFE exome

AF:

0.0674

Gnomad OTH exome

AF:

0.0745

GnomAD4 exome

AF:

0.0691

AC:

99955

AN:

1447506

Hom.:

3999

Cov.:

AF XY:

0.0675

AC XY:

48586

AN XY:

719624

show subpopulations

Gnomad4 AFR exome

AF:

0.174

Gnomad4 AMR exome

AF:

0.153

Gnomad4 ASJ exome

AF:

0.0683

Gnomad4 EAS exome

AF:

0.000558

Gnomad4 SAS exome

AF:

0.0438

Gnomad4 FIN exome

AF:

0.0682

Gnomad4 NFE exome

AF:

0.0670

Gnomad4 OTH exome

AF:

0.0704

GnomAD4 genome

AF:

0.0988

AC:

15026

AN:

152010

Hom.:

945

Cov.:

AF XY:

0.0980

AC XY:

7285

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.171

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.0709

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0458

Gnomad4 FIN

AF:

0.0603

Gnomad4 NFE

AF:

0.0673

Gnomad4 OTH

AF:

0.103

Alfa

AF:

0.0713

Hom.:

664

Bravo

AF:

0.107

TwinsUK

AF:

0.0658

AC:

244

ALSPAC

AF:

0.0690

AC:

266

ESP6500AA

AF:

0.165

AC:

725

ESP6500EA

AF:

0.0682

AC:

586

ExAC

AF:

0.0766

AC:

9293

Asia WGS

AF:

0.0400

AC:

140

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.097

BayesDel_addAF

Benign

-0.66

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.026

.;T

Eigen

Benign

-0.0077

Eigen_PC

Benign

-0.0029

FATHMM_MKL

Pathogenic

0.98

LIST_S2

Uncertain

0.91

D;T

MetaRNN

Benign

0.0018

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Pathogenic

3.0

M;M

PrimateAI

Benign

0.41

PROVEAN

Pathogenic

-5.4

D;D

REVEL

Benign

0.17

Sift

Uncertain

0.0020

D;T

Sift4G

Benign

0.12

T;T

Polyphen

0.73

P;B

Vest4

0.21

MPC

0.10

ClinPred

0.094

GERP RS

4.1

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.094

gMVP

0.17

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over