chr16-31109261-G-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_005881.4(BCKDK):c.38G>C(p.Gly13Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,404,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005881.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCKDK | NM_005881.4 | c.38G>C | p.Gly13Ala | missense_variant | 2/12 | ENST00000219794.11 | |
BCKDK | NM_001122957.4 | c.38G>C | p.Gly13Ala | missense_variant | 2/11 | ||
BCKDK | NM_001271926.3 | c.38G>C | p.Gly13Ala | missense_variant | 2/10 | ||
BCKDK | XM_017022859.2 | c.38G>C | p.Gly13Ala | missense_variant | 2/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCKDK | ENST00000219794.11 | c.38G>C | p.Gly13Ala | missense_variant | 2/12 | 1 | NM_005881.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000516 AC: 10AN: 193926Hom.: 0 AF XY: 0.0000837 AC XY: 9AN XY: 107566
GnomAD4 exome AF: 0.0000192 AC: 27AN: 1404756Hom.: 0 Cov.: 33 AF XY: 0.0000274 AC XY: 19AN XY: 694444
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Oct 23, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at