2-237324809-C-T
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_004369.4(COL6A3):c.9499G>A(p.Ala3167Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000168 in 1,613,378 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 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
Publications
- Bethlem myopathy 1AInheritance: AD, AR, SD Classification: DEFINITIVE, STRONG Submitted by: Genomics England PanelApp, Ambry Genetics
- collagen 6-related myopathyInheritance: AD, AR Classification: DEFINITIVE Submitted by: ClinGen
- Ullrich congenital muscular dystrophy 1CInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- dystonia 27Inheritance: AR Classification: STRONG, SUPPORTIVE, LIMITED, NO_KNOWN Submitted by: Illumina, Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics, Orphanet
- Ullrich congenital muscular dystrophy 1AInheritance: AR, AD, SD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp
- Bethlem myopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Ullrich congenital muscular dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Likely_benign. The variant received -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.9499G>A | p.Ala3167Thr | missense_variant | Exon 44 of 44 | ENST00000295550.9 | NP_004360.2 | |
COL6A3 | NM_057167.4 | c.8881G>A | p.Ala2961Thr | missense_variant | Exon 43 of 43 | NP_476508.2 | ||
COL6A3 | NM_057166.5 | c.7678G>A | p.Ala2560Thr | missense_variant | Exon 41 of 41 | NP_476507.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152000Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000403 AC: 10AN: 248104 AF XY: 0.0000596 show subpopulations
GnomAD4 exome AF: 0.000181 AC: 265AN: 1461260Hom.: 0 Cov.: 31 AF XY: 0.000169 AC XY: 123AN XY: 726904 show subpopulations
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74370 show subpopulations
ClinVar
Submissions by phenotype
not provided Uncertain:1
- -
Bethlem myopathy 1A Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at