rs370664069
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004369.4(COL6A3):c.3055G>A(p.Gly1019Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004369.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.3055G>A | p.Gly1019Arg | missense_variant | 7/44 | ENST00000295550.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.3055G>A | p.Gly1019Arg | missense_variant | 7/44 | 1 | NM_004369.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000855 AC: 13AN: 152066Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000917 AC: 23AN: 250784Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135612
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1461794Hom.: 0 Cov.: 32 AF XY: 0.0000206 AC XY: 15AN XY: 727204
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152066Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74280
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jun 01, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Sep 24, 2020 | - - |
Ullrich congenital muscular dystrophy 1A;C4225336:Dystonia 27;CN029274:Bethlem myopathy 1A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
COL6A3-related disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 10, 2023 | The COL6A3 c.3055G>A variant is predicted to result in the amino acid substitution p.Gly1019Arg. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.038% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-238285430-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at