chr16-31111229-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005881.4(BCKDK):c.845+10C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00159 in 1,614,134 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_005881.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCKDK | NM_005881.4 | c.845+10C>T | intron_variant | Intron 9 of 11 | ENST00000219794.11 | NP_005872.2 | ||
BCKDK | NM_001122957.4 | c.845+10C>T | intron_variant | Intron 9 of 10 | NP_001116429.1 | |||
BCKDK | NM_001271926.3 | c.845+10C>T | intron_variant | Intron 9 of 9 | NP_001258855.1 | |||
BCKDK | XM_017022859.2 | c.845+10C>T | intron_variant | Intron 9 of 11 | XP_016878348.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00883 AC: 1343AN: 152158Hom.: 14 Cov.: 33
GnomAD3 exomes AF: 0.00202 AC: 507AN: 251266Hom.: 9 AF XY: 0.00138 AC XY: 188AN XY: 135806
GnomAD4 exome AF: 0.000832 AC: 1216AN: 1461858Hom.: 18 Cov.: 32 AF XY: 0.000668 AC XY: 486AN XY: 727228
GnomAD4 genome AF: 0.00883 AC: 1345AN: 152276Hom.: 14 Cov.: 33 AF XY: 0.00861 AC XY: 641AN XY: 74450
ClinVar
Submissions by phenotype
not specified Benign:2
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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not provided Benign:1
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Branched-chain keto acid dehydrogenase kinase deficiency Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at