10-69802497-CG-C
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_001368882.1(COL13A1):c.76delG(p.Val26TrpfsTer23) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000196 in 1,534,494 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_001368882.1 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL13A1 | NM_001368882.1 | c.76delG | p.Val26TrpfsTer23 | frameshift_variant | Exon 1 of 41 | ENST00000645393.2 | NP_001355811.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL13A1 | ENST00000645393.2 | c.76delG | p.Val26TrpfsTer23 | frameshift_variant | Exon 1 of 41 | NM_001368882.1 | ENSP00000496051.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152102Hom.: 0 Cov.: 33
GnomAD4 exome AF: 7.23e-7 AC: 1AN: 1382392Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 682660
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152102Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74290
ClinVar
Submissions by phenotype
not provided Pathogenic:1
For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with COL13A1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Val26Trpfs*23) in the COL13A1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in COL13A1 are known to be pathogenic (PMID: 26626625). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at