rs139648899
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_ModerateBP6
The NM_001848.3(COL6A1):c.409C>G(p.Leu137Val) variant causes a missense change. The variant allele was found at a frequency of 0.000169 in 1,611,006 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. L137L) has been classified as Likely benign.
Frequency
Consequence
NM_001848.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.409C>G | p.Leu137Val | missense_variant | 3/35 | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.409C>G | p.Leu137Val | missense_variant | 3/35 | 1 | NM_001848.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 23AN: 152264Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.000251 AC: 62AN: 247166Hom.: 0 AF XY: 0.000223 AC XY: 30AN XY: 134536
GnomAD4 exome AF: 0.000171 AC: 250AN: 1458742Hom.: 1 Cov.: 33 AF XY: 0.000160 AC XY: 116AN XY: 725808
GnomAD4 genome ? AF: 0.000151 AC: 23AN: 152264Hom.: 0 Cov.: 35 AF XY: 0.0000941 AC XY: 7AN XY: 74392
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 22, 2016 | - - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at