chr19-41397839-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000709.4(BCKDHA):c.12G>A(p.Ala4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A4A) has been classified as Likely benign.
Frequency
Consequence
NM_000709.4 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 |
---|---|---|---|---|---|---|---|
BCKDHA | NM_000709.4 | c.12G>A | p.Ala4= | synonymous_variant | 1/9 | ENST00000269980.7 | |
BCKDHA | NM_001164783.2 | c.12G>A | p.Ala4= | synonymous_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCKDHA | ENST00000269980.7 | c.12G>A | p.Ala4= | synonymous_variant | 1/9 | 1 | NM_000709.4 | P1 | |
BCKDHA | ENST00000457836.6 | c.12G>A | p.Ala4= | synonymous_variant | 1/9 | 2 | |||
BCKDHA | ENST00000542943.5 | c.12G>A | p.Ala4= | synonymous_variant | 1/7 | 5 | |||
BCKDHA | ENST00000538423.5 | n.32G>A | non_coding_transcript_exon_variant | 1/5 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Maple syrup urine disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.