rs148252611
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_004369.4(COL6A3):c.6289C>T(p.Arg2097Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000756 in 1,613,776 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2097Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_004369.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.6289C>T | p.Arg2097Trp | missense_variant | 18/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.5671C>T | p.Arg1891Trp | missense_variant | 17/43 | ||
COL6A3 | NM_057166.5 | c.4468C>T | p.Arg1490Trp | missense_variant | 15/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.6289C>T | p.Arg2097Trp | missense_variant | 18/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.4468C>T | p.Arg1490Trp | missense_variant | 15/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.5671C>T | p.Arg1891Trp | missense_variant | 17/43 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000803 AC: 20AN: 249080Hom.: 0 AF XY: 0.0000890 AC XY: 12AN XY: 134884
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461486Hom.: 0 Cov.: 34 AF XY: 0.0000853 AC XY: 62AN XY: 727026
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152290Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74462
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 23, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 08, 2021 | - - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at