11-112179356-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_031938.7(BCO2):c.167C>T(p.Pro56Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000359 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031938.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BCO2 | ENST00000357685.11 | c.167C>T | p.Pro56Leu | missense_variant | Exon 2 of 12 | 1 | NM_031938.7 | ENSP00000350314.5 | ||
ENSG00000255292 | ENST00000532699.1 | n.*55+8682C>T | intron_variant | Intron 5 of 5 | 3 | ENSP00000456434.1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152102Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251476Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135918
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000330 AC XY: 24AN XY: 727246
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152102Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.167C>T (p.P56L) alteration is located in exon 2 (coding exon 2) of the BCO2 gene. This alteration results from a C to T substitution at nucleotide position 167, causing the proline (P) at amino acid position 56 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at