rs113896755
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 6P and 1B. PM1PM2PP3_ModerateBP6
The NM_004369.4(COL6A3):c.6263C>T(p.Pro2088Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000793 in 1,613,996 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P2088P) has been classified as Likely benign.
Frequency
Consequence
NM_004369.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.6263C>T | p.Pro2088Leu | missense_variant | 17/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.5645C>T | p.Pro1882Leu | missense_variant | 16/43 | ||
COL6A3 | NM_057166.5 | c.4442C>T | p.Pro1481Leu | missense_variant | 14/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.6263C>T | p.Pro2088Leu | missense_variant | 17/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.4442C>T | p.Pro1481Leu | missense_variant | 14/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.5645C>T | p.Pro1882Leu | missense_variant | 16/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251322Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135862
GnomAD4 exome AF: 0.0000732 AC: 107AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727244
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74284
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Aug 14, 2023 | - - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
Collagen 6-related myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 28, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at