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
Consequence
NM_000709.4 missense
Scores
Clinical Significance
Conservation
Publications
- maple syrup urine diseaseInheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- maple syrup urine disease type 1AInheritance: AR Classification: DEFINITIVE Submitted by: G2P, Myriad Women’s Health, ClinGen
- classic maple syrup urine diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- intermediate maple syrup urine diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- intermittent maple syrup urine diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- thiamine-responsive maple syrup urine diseaseInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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BCKDHA | ENST00000269980.7 | c.116C>A | p.Pro39His | missense_variant | Exon 2 of 9 | 1 | NM_000709.4 | ENSP00000269980.2 | ||
ENSG00000255730 | ENST00000540732.3 | c.218C>A | p.Pro73His | missense_variant | Exon 3 of 10 | 2 | ENSP00000443246.1 |
Frequencies
GnomAD3 genomes AF: 0.0890 AC: 13543AN: 152128Hom.: 765 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0988 AC: 24826AN: 251376 AF XY: 0.104 show subpopulations
GnomAD4 exome AF: 0.125 AC: 183247AN: 1461826Hom.: 12540 Cov.: 34 AF XY: 0.126 AC XY: 91343AN XY: 727218 show subpopulations
GnomAD4 genome AF: 0.0889 AC: 13541AN: 152246Hom.: 764 Cov.: 32 AF XY: 0.0861 AC XY: 6409AN XY: 74434 show subpopulations
ClinVar
Submissions by phenotype
not specified Benign:3
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. -
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Maple syrup urine disease Benign:3
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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
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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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at