chr6-80106708-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_183050.4(BCKDHB):āc.15G>Cā(p.Ala5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000903 in 1,551,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. A5A) has been classified as Likely benign.
Frequency
Consequence
NM_183050.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCKDHB | NM_183050.4 | c.15G>C | p.Ala5= | synonymous_variant | 1/10 | ENST00000320393.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCKDHB | ENST00000320393.9 | c.15G>C | p.Ala5= | synonymous_variant | 1/10 | 1 | NM_183050.4 | P1 | |
BCKDHB | ENST00000356489.9 | c.15G>C | p.Ala5= | synonymous_variant | 1/11 | 1 | P1 | ||
BCKDHB | ENST00000369760.8 | c.15G>C | p.Ala5= | synonymous_variant | 1/6 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000674 AC: 1AN: 148374Hom.: 0 AF XY: 0.0000125 AC XY: 1AN XY: 79846
GnomAD4 exome AF: 0.00000929 AC: 13AN: 1398860Hom.: 0 Cov.: 32 AF XY: 0.0000116 AC XY: 8AN XY: 690346
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
Maple syrup urine disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at