2-237364358-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_004369.4(COL6A3):c.5909G>A(p.Arg1970His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000254 in 1,613,400 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1970C) 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A3 | NM_004369.4 | c.5909G>A | p.Arg1970His | missense_variant | 13/44 | ENST00000295550.9 | |
COL6A3 | NM_057167.4 | c.5291G>A | p.Arg1764His | missense_variant | 12/43 | ||
COL6A3 | NM_057166.5 | c.4088G>A | p.Arg1363His | missense_variant | 10/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A3 | ENST00000295550.9 | c.5909G>A | p.Arg1970His | missense_variant | 13/44 | 1 | NM_004369.4 | P1 | |
COL6A3 | ENST00000472056.5 | c.4088G>A | p.Arg1363His | missense_variant | 10/41 | 1 | |||
COL6A3 | ENST00000353578.9 | c.5291G>A | p.Arg1764His | missense_variant | 12/43 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251366Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135872
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1461184Hom.: 1 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 726930
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at