rs745434198
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PP2PP3_StrongPP5_Moderate
The NM_080680.3(COL11A2):c.4430G>T(p.Gly1477Val) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.000000684 in 1,461,784 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_080680.3 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL11A2 | NM_080680.3 | c.4430G>T | p.Gly1477Val | missense_variant, splice_region_variant | 62/66 | ENST00000341947.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL11A2 | ENST00000341947.7 | c.4430G>T | p.Gly1477Val | missense_variant, splice_region_variant | 62/66 | 5 | NM_080680.3 | P4 | |
COL11A2 | ENST00000374708.8 | c.4172G>T | p.Gly1391Val | missense_variant, splice_region_variant | 60/64 | 5 | A1 | ||
COL11A2 | ENST00000683572.1 | n.236G>T | splice_region_variant, non_coding_transcript_exon_variant | 5/9 | |||||
COL11A2 | ENST00000477772.1 | n.273-167G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249170Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135080
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461784Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 727194
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Sensorineural hearing loss disorder Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Mar 17, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at