rs111927395
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_004369.4(COL6A3):āc.6902T>Cā(p.Val2301Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000052 in 1,614,082 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. 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. V2301F) has been classified as Uncertain significance.
Frequency
Consequence
NM_004369.4 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 |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.6902T>C | p.Val2301Ala | missense_variant | 29/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.6284T>C | p.Val2095Ala | missense_variant | 28/43 | ||
COL6A3 | NM_057166.5 | c.5081T>C | p.Val1694Ala | missense_variant | 26/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.6902T>C | p.Val2301Ala | missense_variant | 29/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.5081T>C | p.Val1694Ala | missense_variant | 26/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.6284T>C | p.Val2095Ala | missense_variant | 28/43 | 5 | |||
COL6A3 | ENST00000491769.1 | n.1156T>C | non_coding_transcript_exon_variant | 6/20 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152090Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251308Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135812
GnomAD4 exome AF: 0.0000527 AC: 77AN: 1461874Hom.: 0 Cov.: 32 AF XY: 0.0000523 AC XY: 38AN XY: 727236
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74402
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 07, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jul 01, 2024 | - - |
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at