rs545819982
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004369.4(COL6A3):c.7513G>A(p.Gly2505Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000545 in 1,614,192 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. G2505V) has been classified as Uncertain significance.
Frequency
Consequence
NM_004369.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.7513G>A | p.Gly2505Arg | missense_variant | 36/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.6895G>A | p.Gly2299Arg | missense_variant | 35/43 | ||
COL6A3 | NM_057166.5 | c.5692G>A | p.Gly1898Arg | missense_variant | 33/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.7513G>A | p.Gly2505Arg | missense_variant | 36/44 | 1 | NM_004369.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000875 AC: 22AN: 251410Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135862
GnomAD4 exome AF: 0.0000363 AC: 53AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727248
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74470
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Mar 25, 2022 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Sep 23, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 09, 2023 | Reported in a patient with a clinical diagnosis of limb girdle muscular dystrophy (Nallamilli et al., 2018); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 33964895, 30564623) - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at