rs140027285
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_001849.4(COL6A2):c.1161C>T(p.Ile387Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00342 in 1,611,530 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001849.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.1161C>T | p.Ile387Ile | synonymous_variant | Exon 13 of 28 | ENST00000300527.9 | NP_001840.3 | |
COL6A2 | NM_058174.3 | c.1161C>T | p.Ile387Ile | synonymous_variant | Exon 13 of 28 | NP_478054.2 | ||
COL6A2 | NM_058175.3 | c.1161C>T | p.Ile387Ile | synonymous_variant | Exon 13 of 28 | NP_478055.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.1161C>T | p.Ile387Ile | synonymous_variant | Exon 13 of 28 | 1 | NM_001849.4 | ENSP00000300527.4 | ||
COL6A2 | ENST00000397763.6 | c.1161C>T | p.Ile387Ile | synonymous_variant | Exon 13 of 28 | 5 | ENSP00000380870.1 | |||
COL6A2 | ENST00000409416.6 | c.1161C>T | p.Ile387Ile | synonymous_variant | Exon 12 of 27 | 5 | ENSP00000387115.1 |
Frequencies
GnomAD3 genomes AF: 0.00224 AC: 341AN: 152236Hom.: 1 Cov.: 34
GnomAD3 exomes AF: 0.00249 AC: 609AN: 244506Hom.: 6 AF XY: 0.00260 AC XY: 345AN XY: 132886
GnomAD4 exome AF: 0.00355 AC: 5176AN: 1459176Hom.: 15 Cov.: 32 AF XY: 0.00344 AC XY: 2500AN XY: 725726
GnomAD4 genome AF: 0.00224 AC: 341AN: 152354Hom.: 1 Cov.: 34 AF XY: 0.00208 AC XY: 155AN XY: 74500
ClinVar
Submissions by phenotype
not provided Benign:3
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This variant is associated with the following publications: (PMID: 30564623) -
COL6A2: BP4, BP7, BS2 -
not specified Benign:2
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Myosclerosis Benign:1
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Collagen 6-related myopathy Benign:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at