chr21-46116045-G-A
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PS1PM1PM2PM5PP3_StrongPP5_Moderate
The NM_001849.4(COL6A2):c.892G>A(p.Gly298Arg) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G298A) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001849.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL6A2 | NM_001849.4 | c.892G>A | p.Gly298Arg | missense_variant | 7/28 | ENST00000300527.9 | |
COL6A2 | NM_058174.3 | c.892G>A | p.Gly298Arg | missense_variant | 7/28 | ENST00000397763.6 | |
COL6A2 | NM_058175.3 | c.892G>A | p.Gly298Arg | missense_variant | 7/28 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL6A2 | ENST00000300527.9 | c.892G>A | p.Gly298Arg | missense_variant | 7/28 | 1 | NM_001849.4 | P1 | |
COL6A2 | ENST00000397763.6 | c.892G>A | p.Gly298Arg | missense_variant | 7/28 | 5 | NM_058174.3 | ||
COL6A2 | ENST00000409416.6 | c.892G>A | p.Gly298Arg | missense_variant | 6/27 | 5 | |||
COL6A2 | ENST00000485591.1 | n.548G>A | non_coding_transcript_exon_variant | 3/7 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Myopathy Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 14, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at