rs778962979
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP3_ModerateBP6
The NM_080680.3(COL11A2):c.4786C>T(p.Arg1596Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000253 in 1,580,628 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_080680.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.4786C>T | p.Arg1596Trp | missense_variant | Exon 64 of 66 | ENST00000341947.7 | NP_542411.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947.7 | c.4786C>T | p.Arg1596Trp | missense_variant | Exon 64 of 66 | 5 | NM_080680.3 | ENSP00000339915.2 | ||
COL11A2 | ENST00000374708.8 | c.4528C>T | p.Arg1510Trp | missense_variant | Exon 62 of 64 | 5 | ENSP00000363840.4 | |||
COL11A2 | ENST00000477772.1 | n.576C>T | non_coding_transcript_exon_variant | Exon 7 of 9 | 2 | |||||
COL11A2 | ENST00000683572.1 | n.592C>T | non_coding_transcript_exon_variant | Exon 7 of 9 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152098Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000500 AC: 1AN: 199846Hom.: 0 AF XY: 0.00000938 AC XY: 1AN XY: 106590
GnomAD4 exome AF: 0.00000210 AC: 3AN: 1428412Hom.: 0 Cov.: 32 AF XY: 0.00000424 AC XY: 3AN XY: 707274
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152216Hom.: 0 Cov.: 31 AF XY: 0.0000134 AC XY: 1AN XY: 74422
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Arg1596Trp variant in COL11A2 has not been previously reported in individu als with hearing loss, but was identified in 1/8338 South Asian chromosomes by t he Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs7 78962979). Computational prediction tools and conservation analyses suggest tha t the p.Arg1596Trp variant may impact the protein, though this information is no t predictive enough to determine pathogenicity. In summary, the clinical signifi cance of the p.Arg1596Trp variant is uncertain. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at