rs777696289
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PM4_Supporting
The NM_001849.4(COL6A2):c.2738_2740delCCT(p.Ser913del) variant causes a disruptive inframe deletion change. The variant allele was found at a frequency of 0.0000131 in 1,597,018 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001849.4 disruptive_inframe_deletion
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 |
---|---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.2738_2740delCCT | p.Ser913del | disruptive_inframe_deletion | Exon 28 of 28 | ENST00000300527.9 | NP_001840.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151726Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000137 AC: 3AN: 218854Hom.: 0 AF XY: 0.0000250 AC XY: 3AN XY: 119804
GnomAD4 exome AF: 0.0000138 AC: 20AN: 1445292Hom.: 0 AF XY: 0.0000125 AC XY: 9AN XY: 718218
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151726Hom.: 0 Cov.: 34 AF XY: 0.0000135 AC XY: 1AN XY: 74104
ClinVar
Submissions by phenotype
not provided Uncertain:2
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Not observed at significant frequency in large population cohorts (gnomAD); In-frame deletion of one amino acid in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function; Identified in a family with a clinical diagnosis of Ullrich congenital muscular dystrophy in published literature (PMID: 36982625); This variant is associated with the following publications: (PMID: 36982625) -
Bethlem myopathy 1A 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. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. ClinVar contains an entry for this variant (Variation ID: 289580). This variant has not been reported in the literature in individuals affected with COL6A2-related conditions. This variant is present in population databases (rs777696289, gnomAD 0.003%). This variant, c.2738_2740del, results in the deletion of 1 amino acid(s) of the COL6A2 protein (p.Ser913del), but otherwise preserves the integrity of the reading frame. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at