20-62830443-T-TGG
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001853.4(COL9A3):c.1215+35_1215+36dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000254 in 1,574,202 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 28)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
COL9A3
NM_001853.4 intron
NM_001853.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.75
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 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL9A3 | NM_001853.4 | c.1215+35_1215+36dup | intron_variant | ENST00000649368.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL9A3 | ENST00000649368.1 | c.1215+35_1215+36dup | intron_variant | NM_001853.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000660 AC: 1AN: 151596Hom.: 0 Cov.: 28
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GnomAD3 exomes AF: 0.00000539 AC: 1AN: 185700Hom.: 0 AF XY: 0.0000100 AC XY: 1AN XY: 99708
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GnomAD4 exome AF: 0.00000211 AC: 3AN: 1422488Hom.: 0 Cov.: 35 AF XY: 0.00000142 AC XY: 1AN XY: 704114
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GnomAD4 genome ? AF: 0.00000659 AC: 1AN: 151714Hom.: 0 Cov.: 28 AF XY: 0.0000135 AC XY: 1AN XY: 74160
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at