chr19-41422992-G-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000709.4(BCKDHA):c.996-6G>C variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000056 in 1,608,112 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000709.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCKDHA | NM_000709.4 | c.996-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000269980.7 | |||
BCKDHA | NM_001164783.2 | c.993-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCKDHA | ENST00000269980.7 | c.996-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000709.4 | P1 | |||
BCKDHA | ENST00000457836.6 | c.999G>C | p.Leu333= | synonymous_variant | 8/9 | 2 | |||
BCKDHA | ENST00000542943.5 | c.909-6G>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000420 AC: 1AN: 238176Hom.: 0 AF XY: 0.00000776 AC XY: 1AN XY: 128900
GnomAD4 exome AF: 0.00000481 AC: 7AN: 1456078Hom.: 0 Cov.: 35 AF XY: 0.00000553 AC XY: 4AN XY: 723746
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152034Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74242
ClinVar
Submissions by phenotype
Maple syrup urine disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 05, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at