rs727502941
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP2PP3_Strong
The NM_080680.3(COL11A2):c.2693G>A(p.Gly898Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000248 in 1,612,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. G898G) has been classified as Likely benign.
Frequency
Consequence
NM_080680.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.2693G>A | p.Gly898Glu | missense_variant | 37/66 | ENST00000341947.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947.7 | c.2693G>A | p.Gly898Glu | missense_variant | 37/66 | 5 | NM_080680.3 | P4 | |
COL11A2 | ENST00000374708.8 | c.2435G>A | p.Gly812Glu | missense_variant | 35/64 | 5 | A1 | ||
COL11A2 | ENST00000361917.6 | c.1268G>A | p.Gly423Glu | missense_variant | 24/24 | 5 | |||
COL11A2 | ENST00000477772.1 | n.272+3618G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000409 AC: 1AN: 244256Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 132550
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460864Hom.: 0 Cov.: 48 AF XY: 0.00000138 AC XY: 1AN XY: 726658
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74292
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 21, 2014 | The Gly898Glu variant in COL11A2 has not been previously reported in individuals with hearing loss and was absent from large population studies. Computational p rediction tools and conservation analyses suggest that the Gly898Glu variant may impact the protein, though this information is not predictive enough to determi ne pathogenicity. In summary, the clinical significance of the Gly898Glu variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at