rs61735827
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001849.4(COL6A2):c.1251C>T(p.Arg417=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00121 in 1,611,942 control chromosomes in the GnomAD database, including 14 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. R417R) has been classified as Likely benign.
Frequency
Consequence
NM_001849.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.1251C>T | p.Arg417= | synonymous_variant | 14/28 | ENST00000300527.9 | |
COL6A2 | NM_058174.3 | c.1251C>T | p.Arg417= | synonymous_variant | 14/28 | ENST00000397763.6 | |
COL6A2 | NM_058175.3 | c.1251C>T | p.Arg417= | synonymous_variant | 14/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.1251C>T | p.Arg417= | synonymous_variant | 14/28 | 1 | NM_001849.4 | P1 | |
COL6A2 | ENST00000397763.6 | c.1251C>T | p.Arg417= | synonymous_variant | 14/28 | 5 | NM_058174.3 | ||
COL6A2 | ENST00000409416.6 | c.1251C>T | p.Arg417= | synonymous_variant | 13/27 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00105 AC: 159AN: 152108Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00155 AC: 382AN: 245882Hom.: 7 AF XY: 0.00149 AC XY: 200AN XY: 134052
GnomAD4 exome AF: 0.00123 AC: 1791AN: 1459716Hom.: 13 Cov.: 35 AF XY: 0.00123 AC XY: 890AN XY: 726192
GnomAD4 genome ? AF: 0.00104 AC: 159AN: 152226Hom.: 1 Cov.: 34 AF XY: 0.00107 AC XY: 80AN XY: 74420
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Mar 01, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 26, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Myosclerosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Collagen 6-related myopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2024 | COL6A2: BP4, BP7 - |
COL6A2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 03, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Ullrich congenital muscular dystrophy 1A;C1850671:Myosclerosis;CN029274:Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | May 23, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at