rs773668391
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBP7
The NM_001849.4(COL6A2):c.2235G>T(p.Arg745=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,612,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R745R) has been classified as Likely benign.
Frequency
Consequence
NM_001849.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.2235G>T | p.Arg745= | synonymous_variant | 26/28 | ENST00000300527.9 | |
COL6A2 | NM_058174.3 | c.2235G>T | p.Arg745= | synonymous_variant | 26/28 | ENST00000397763.6 | |
COL6A2 | NM_058175.3 | c.2235G>T | p.Arg745= | synonymous_variant | 26/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.2235G>T | p.Arg745= | synonymous_variant | 26/28 | 1 | NM_001849.4 | P1 | |
COL6A2 | ENST00000397763.6 | c.2235G>T | p.Arg745= | synonymous_variant | 26/28 | 5 | NM_058174.3 | ||
COL6A2 | ENST00000409416.6 | c.2235G>T | p.Arg745= | synonymous_variant | 25/27 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 250842Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135760
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460730Hom.: 0 Cov.: 37 AF XY: 0.00000826 AC XY: 6AN XY: 726682
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 26, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at