rs147194375
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_001849.4(COL6A2):āc.1614C>Gā(p.Gly538=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,613,146 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 (ā ). Synonymous variant affecting the same amino acid position (i.e. G538G) has been classified as Likely benign.
Frequency
Consequence
NM_001849.4 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.1614C>G | p.Gly538= | synonymous_variant | 21/28 | ENST00000300527.9 | |
COL6A2 | NM_058174.3 | c.1614C>G | p.Gly538= | synonymous_variant | 21/28 | ENST00000397763.6 | |
COL6A2 | NM_058175.3 | c.1614C>G | p.Gly538= | synonymous_variant | 21/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.1614C>G | p.Gly538= | synonymous_variant | 21/28 | 1 | NM_001849.4 | P1 | |
COL6A2 | ENST00000397763.6 | c.1614C>G | p.Gly538= | synonymous_variant | 21/28 | 5 | NM_058174.3 | ||
COL6A2 | ENST00000409416.6 | c.1614C>G | p.Gly538= | synonymous_variant | 20/27 | 5 | |||
COL6A2 | ENST00000413758.1 | c.237C>G | p.Gly79= | synonymous_variant | 6/11 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250316Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135744
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461014Hom.: 0 Cov.: 36 AF XY: 0.00000275 AC XY: 2AN XY: 726808
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152132Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74320
ClinVar
Submissions by phenotype
Bethlem myopathy 1A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 27, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at