Variant 11-116760826-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_032725.4(BUD13):c.1163C>G(p.Ser388Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0107 in 1,614,144 control chromosomes in the GnomAD database, including 133 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.0087 ( 18 hom., cov: 32)

Exomes 𝑓: 0.011 ( 115 hom. )

Consequence

BUD13
NM_032725.4 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 5.68

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0069322884).

BP6

Variant 11-116760826-G-C is Benign according to our data. Variant chr11-116760826-G-C is described in ClinVar as [Benign]. Clinvar id is 773014.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0109 (15871/1461854) while in subpopulation MID AF= 0.0442 (255/5766). AF 95% confidence interval is 0.0398. There are 115 homozygotes in gnomad4_exome. There are 7978 alleles in male gnomad4_exome subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 18 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
BUD13	NM_032725.4 linkuse as main transcript	c.1163C>G	p.Ser388Cys	missense_variant	5/10	ENST00000260210.5	NP_116114.1
BUD13	NM_001159736.2 linkuse as main transcript	c.761C>G	p.Ser254Cys	missense_variant	5/10		NP_001153208.1
BUD13	XM_011543035.3 linkuse as main transcript	c.1064C>G	p.Ser355Cys	missense_variant	5/10		XP_011541337.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BUD13	ENST00000260210.5 linkuse as main transcript	c.1163C>G	p.Ser388Cys	missense_variant	5/10	1	NM_032725.4	ENSP00000260210	P2	Q9BRD0-1
BUD13	ENST00000375445.7 linkuse as main transcript	c.761C>G	p.Ser254Cys	missense_variant	5/10	1		ENSP00000364594	A2	Q9BRD0-2
BUD13	ENST00000419189.1 linkuse as main transcript	c.284+1727C>G		intron_variant, NMD_transcript_variant		5		ENSP00000415748

Frequencies

GnomAD3 genomes

AF:

0.00878

AC:

1336

AN:

152172

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00222

Gnomad AMI

AF:

0.0714

Gnomad AMR

AF:

0.00798

Gnomad ASJ

AF:

0.00691

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00539

Gnomad FIN

AF:

0.0122

Gnomad MID

AF:

0.0380

Gnomad NFE

AF:

0.0123

Gnomad OTH

AF:

0.0124

GnomAD3 exomes

AF:

0.00964

AC:

2425

AN:

251490

Hom.:

AF XY:

0.0100

AC XY:

1359

AN XY:

135922

show subpopulations

Gnomad AFR exome

AF:

0.00203

Gnomad AMR exome

AF:

0.00543

Gnomad ASJ exome

AF:

0.00565

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00438

Gnomad FIN exome

AF:

0.0127

Gnomad NFE exome

AF:

0.0144

Gnomad OTH exome

AF:

0.0158

GnomAD4 exome

AF:

0.0109

AC:

15871

AN:

1461854

Hom.:

115

Cov.:

AF XY:

0.0110

AC XY:

7978

AN XY:

727234

show subpopulations

Gnomad4 AFR exome

AF:

0.00278

Gnomad4 AMR exome

AF:

0.00550

Gnomad4 ASJ exome

AF:

0.00647

Gnomad4 EAS exome

AF:

0.0000756

Gnomad4 SAS exome

AF:

0.00470

Gnomad4 FIN exome

AF:

0.0122

Gnomad4 NFE exome

AF:

0.0121

Gnomad4 OTH exome

AF:

0.0103

GnomAD4 genome

AF:

0.00875

AC:

1332

AN:

152290

Hom.:

Cov.:

AF XY:

0.00865

AC XY:

644

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00219

Gnomad4 AMR

AF:

0.00797

Gnomad4 ASJ

AF:

0.00691

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00540

Gnomad4 FIN

AF:

0.0122

Gnomad4 NFE

AF:

0.0123

Gnomad4 OTH

AF:

0.0123

Alfa

AF:

0.0108

Hom.:

Bravo

AF:

0.00836

TwinsUK

AF:

0.0111

AC:

ALSPAC

AF:

0.0101

AC:

ESP6500AA

AF:

0.00295

AC:

ESP6500EA

AF:

0.0159

AC:

137

ExAC

AF:

0.00995

AC:

1208

Asia WGS

AF:

0.00404

AC:

AN:

3478

EpiCase

AF:

0.0169

EpiControl

AF:

0.0154

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jun 29, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.18

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.29

CADD

Pathogenic

DANN

Uncertain

0.99

DEOGEN2

Benign

0.19

.;T

Eigen

Pathogenic

0.86

Eigen_PC

Pathogenic

0.83

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.93

D;D

MetaRNN

Benign

0.0069

T;T

MetaSVM

Benign

-0.80

MutationAssessor

Pathogenic

3.6

.;H

MutationTaster

Benign

1.0

D;D

PrimateAI

Benign

0.48

PROVEAN

Uncertain

-3.9

D;D

REVEL

Benign

0.27

Sift

Uncertain

0.0060

D;D

Sift4G

Uncertain

0.0060

D;D

Polyphen

1.0

D;D

Vest4

0.37

MVP

0.66

MPC

0.46

ClinPred

0.050

GERP RS

5.9

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.30

gMVP

0.24

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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