rs11549936

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000709.4(BCKDHA):​c.116C>A​(p.Pro39His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 1,614,072 control chromosomes in the GnomAD database, including 13,304 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P39S) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.089 ( 764 hom., cov: 32)
Exomes 𝑓: 0.13 ( 12540 hom. )

Consequence

BCKDHA
NM_000709.4 missense

Scores

1
17

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -1.80

Publications

18 publications found
Variant links:
Genes affected
BCKDHA (HGNC:986): (branched chain keto acid dehydrogenase E1 subunit alpha) The branched-chain alpha-keto acid (BCAA) dehydrogenase (BCKD) complex is an innter mitochondrial enzyme complex that catalyzes the second major step in the catabolism of the branched-chain amino acids leucine, isoleucine, and valine. The BCKD complex consists of three catalytic components: a heterotetrameric (alpha2-beta2) branched-chain alpha-keto acid decarboxylase (E1), a dihydrolipoyl transacylase (E2), and a dihydrolipoamide dehydrogenase (E3). This gene encodes the alpha subunit of the decarboxylase (E1) component. Mutations in this gene result in maple syrup urine disease, type IA. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
BCKDHA Gene-Disease associations (from GenCC):
  • maple syrup urine disease
    Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
  • maple syrup urine disease type 1A
    Inheritance: AR Classification: DEFINITIVE Submitted by: G2P, Myriad Women’s Health, ClinGen
  • classic maple syrup urine disease
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • intermediate maple syrup urine disease
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • intermittent maple syrup urine disease
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
  • thiamine-responsive maple syrup urine disease
    Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0015936196).
BP6
Variant 19-41410644-C-A is Benign according to our data. Variant chr19-41410644-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 93341.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.13 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BCKDHANM_000709.4 linkc.116C>A p.Pro39His missense_variant Exon 2 of 9 ENST00000269980.7 NP_000700.1 P12694-1A0A024R0K3
BCKDHANM_001164783.2 linkc.116C>A p.Pro39His missense_variant Exon 2 of 9 NP_001158255.1 P12694Q59EI3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
BCKDHAENST00000269980.7 linkc.116C>A p.Pro39His missense_variant Exon 2 of 9 1 NM_000709.4 ENSP00000269980.2 P12694-1
ENSG00000255730ENST00000540732.3 linkc.218C>A p.Pro73His missense_variant Exon 3 of 10 2 ENSP00000443246.1 F5H5P2

Frequencies

GnomAD3 genomes
AF:
0.0890
AC:
13543
AN:
152128
Hom.:
765
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0228
Gnomad AMI
AF:
0.156
Gnomad AMR
AF:
0.100
Gnomad ASJ
AF:
0.137
Gnomad EAS
AF:
0.000386
Gnomad SAS
AF:
0.103
Gnomad FIN
AF:
0.0715
Gnomad MID
AF:
0.101
Gnomad NFE
AF:
0.132
Gnomad OTH
AF:
0.0927
GnomAD2 exomes
AF:
0.0988
AC:
24826
AN:
251376
AF XY:
0.104
show subpopulations
Gnomad AFR exome
AF:
0.0204
Gnomad AMR exome
AF:
0.0629
Gnomad ASJ exome
AF:
0.132
Gnomad EAS exome
AF:
0.000598
Gnomad FIN exome
AF:
0.0741
Gnomad NFE exome
AF:
0.133
Gnomad OTH exome
AF:
0.107
GnomAD4 exome
AF:
0.125
AC:
183247
AN:
1461826
Hom.:
12540
Cov.:
34
AF XY:
0.126
AC XY:
91343
AN XY:
727218
show subpopulations
African (AFR)
AF:
0.0200
AC:
669
AN:
33480
American (AMR)
AF:
0.0664
AC:
2969
AN:
44716
Ashkenazi Jewish (ASJ)
AF:
0.128
AC:
3357
AN:
26134
East Asian (EAS)
AF:
0.000504
AC:
20
AN:
39700
South Asian (SAS)
AF:
0.116
AC:
9997
AN:
86256
European-Finnish (FIN)
AF:
0.0739
AC:
3949
AN:
53408
Middle Eastern (MID)
AF:
0.128
AC:
740
AN:
5764
European-Non Finnish (NFE)
AF:
0.139
AC:
154498
AN:
1111982
Other (OTH)
AF:
0.117
AC:
7048
AN:
60386
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.476
Heterozygous variant carriers
0
9859
19718
29578
39437
49296
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
5504
11008
16512
22016
27520
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.0889
AC:
13541
AN:
152246
Hom.:
764
Cov.:
32
AF XY:
0.0861
AC XY:
6409
AN XY:
74434
show subpopulations
African (AFR)
AF:
0.0228
AC:
946
AN:
41550
American (AMR)
AF:
0.100
AC:
1529
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
0.137
AC:
474
AN:
3472
East Asian (EAS)
AF:
0.000386
AC:
2
AN:
5176
South Asian (SAS)
AF:
0.104
AC:
502
AN:
4828
European-Finnish (FIN)
AF:
0.0715
AC:
759
AN:
10616
Middle Eastern (MID)
AF:
0.102
AC:
30
AN:
294
European-Non Finnish (NFE)
AF:
0.132
AC:
8964
AN:
67996
Other (OTH)
AF:
0.0913
AC:
193
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
639
1277
1916
2554
3193
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
152
304
456
608
760
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.115
Hom.:
2612
Bravo
AF:
0.0874
TwinsUK
AF:
0.142
AC:
528
ALSPAC
AF:
0.148
AC:
571
ESP6500AA
AF:
0.0238
AC:
105
ESP6500EA
AF:
0.136
AC:
1170
ExAC
AF:
0.0983
AC:
11938
Asia WGS
AF:
0.0430
AC:
150
AN:
3478
EpiCase
AF:
0.146
EpiControl
AF:
0.140

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:9
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:3
-
Genetic Services Laboratory, University of Chicago
Significance:Likely benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -

-
PreventionGenetics, part of Exact Sciences
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Aug 17, 2013
Eurofins Ntd Llc (ga)
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Maple syrup urine disease Benign:3
Feb 03, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Jun 10, 2021
Genome-Nilou Lab
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided

- -

Feb 08, 2017
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

Variant summary: The BCKDHA c.116C>A (p.Pro39His) variant involves the alteration of a non-conserved nucleotide. 3/4 in silico tools predict a benign outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 11936/121154 control chromosomes (711 homozygotes) at a frequency of 0.0985192, which is approximately 59 times the estimated maximal expected allele frequency of a pathogenic BCKDHA variant (0.0016771), suggesting this variant is likely a benign polymorphism. This variant has been reported in multiple affected individuals who also carried other variants in BCKDHB that can explain the phenotype, and authors interpreted the variant of interest as silent variant. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign. -

Maple syrup urine disease type 1A Benign:1
Sep 16, 2020
Natera, Inc.
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.062
BayesDel_addAF
Benign
-0.39
T
BayesDel_noAF
Benign
-0.20
CADD
Benign
0.047
DANN
Benign
0.17
DEOGEN2
Benign
0.026
.;T;.
Eigen
Benign
-1.6
Eigen_PC
Benign
-1.7
FATHMM_MKL
Benign
0.0051
N
LIST_S2
Benign
0.13
T;T;T
MetaRNN
Benign
0.0016
T;T;T
MetaSVM
Benign
-0.77
T
MutationAssessor
Benign
-0.55
.;N;.
PhyloP100
-1.8
PrimateAI
Benign
0.33
T
PROVEAN
Benign
0.16
N;N;N
REVEL
Uncertain
0.35
Sift
Benign
0.70
T;T;T
Sift4G
Benign
0.26
T;T;T
Polyphen
0.0
.;B;.
Vest4
0.047
MPC
0.20
ClinPred
0.0013
T
GERP RS
-4.9
PromoterAI
0.0078
Neutral
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.034
gMVP
0.27
Mutation Taster
=99/1
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs11549936; hg19: chr19-41916549; COSMIC: COSV54198869; COSMIC: COSV54198869; API