21-45984397-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_001848.3(COL6A1):c.356C>T(p.Ala119Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,612,732 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A119T) 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 -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A1 | NM_001848.3 | c.356C>T | p.Ala119Val | missense_variant | 3/35 | ENST00000361866.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A1 | ENST00000361866.8 | c.356C>T | p.Ala119Val | missense_variant | 3/35 | 1 | NM_001848.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000525 AC: 8AN: 152266Hom.: 0 Cov.: 35
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249592Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135548
GnomAD4 exome AF: 0.0000253 AC: 37AN: 1460348Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 726502
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152384Hom.: 0 Cov.: 35 AF XY: 0.0000537 AC XY: 4AN XY: 74522
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 25, 2016 | - - |
Bethlem myopathy 1A Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at