10-69802430-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001368882.1(COL13A1):c.7G>A(p.Ala3Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000000743 in 1,345,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001368882.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL13A1 | NM_001368882.1 | c.7G>A | p.Ala3Thr | missense_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.7G>A | p.Ala3Thr | missense_variant | Exon 1 of 41 | NM_001368882.1 | ENSP00000496051.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 7.43e-7 AC: 1AN: 1345208Hom.: 0 Cov.: 30 AF XY: 0.00000151 AC XY: 1AN XY: 663078
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with COL13A1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This sequence change replaces alanine with threonine at codon 3 of the COL13A1 protein (p.Ala3Thr). The alanine residue is weakly conserved and there is a small physicochemical difference between alanine and threonine. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.