rs12038020
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001852.4(COL9A2):c.1792+17G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 1,590,078 control chromosomes in the GnomAD database, including 1,027 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.041 ( 294 hom., cov: 32)
Exomes 𝑓: 0.012 ( 733 hom. )
Consequence
COL9A2
NM_001852.4 intron
NM_001852.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.438
Genes affected
COL9A2 (HGNC:2218): (collagen type IX alpha 2 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. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 1-40302604-C-T is Benign according to our data. Variant chr1-40302604-C-T is described in ClinVar as [Benign]. Clinvar id is 258377.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-40302604-C-T is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL9A2 | NM_001852.4 | c.1792+17G>A | intron_variant | ENST00000372748.8 | NP_001843.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL9A2 | ENST00000372748.8 | c.1792+17G>A | intron_variant | 1 | NM_001852.4 | ENSP00000361834.3 | ||||
COL9A2 | ENST00000482722.5 | n.2095+17G>A | intron_variant | 1 | ||||||
COL9A2 | ENST00000466267.1 | n.757+17G>A | intron_variant | 5 | ||||||
COL9A2 | ENST00000427563.1 | n.*17G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0409 AC: 6225AN: 152070Hom.: 295 Cov.: 32
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GnomAD3 exomes AF: 0.0304 AC: 6505AN: 214164Hom.: 249 AF XY: 0.0264 AC XY: 3074AN XY: 116266
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GnomAD4 exome AF: 0.0117 AC: 16875AN: 1437894Hom.: 733 Cov.: 34 AF XY: 0.0118 AC XY: 8398AN XY: 713898
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GnomAD4 genome AF: 0.0410 AC: 6236AN: 152184Hom.: 294 Cov.: 32 AF XY: 0.0410 AC XY: 3053AN XY: 74408
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 11, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at