20-62817090-CGCTCCT-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PM4BS1_Supporting
The NM_001853.4(COL9A3):c.43_48delCTGCTC(p.Leu15_Leu16del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000563 in 1,242,384 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000056 ( 0 hom. )
Consequence
COL9A3
NM_001853.4 conservative_inframe_deletion
NM_001853.4 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.123
Genes affected
COL9A3 (HGNC:2219): (collagen type IX alpha 3 chain) This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_001853.4.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.0000563 (70/1242384) while in subpopulation MID AF= 0.00115 (4/3474). AF 95% confidence interval is 0.000393. There are 0 homozygotes in gnomad4_exome. There are 43 alleles in male gnomad4_exome subpopulation. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL9A3 | ENST00000649368.1 | c.43_48delCTGCTC | p.Leu15_Leu16del | conservative_inframe_deletion | Exon 1 of 32 | NM_001853.4 | ENSP00000496793.1 | |||
COL9A3 | ENST00000477612.5 | n.75-460_75-455delCTGCTC | intron_variant | Intron 1 of 11 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
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33
GnomAD3 exomes AF: 0.0000123 AC: 1AN: 81068Hom.: 0 AF XY: 0.0000213 AC XY: 1AN XY: 46948
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GnomAD4 exome AF: 0.0000563 AC: 70AN: 1242384Hom.: 0 AF XY: 0.0000702 AC XY: 43AN XY: 612634
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GnomAD4 genome Cov.: 33
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 30, 2024 | This variant, c.43_48del, results in the deletion of 2 amino acid(s) of the COL9A3 protein (p.Leu15_Leu16del), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with COL9A3-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at