rs2273195
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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.249+36C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0667 in 1,610,956 control chromosomes in the GnomAD database, including 5,441 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.11 ( 1239 hom., cov: 32)
Exomes 𝑓: 0.063 ( 4202 hom. )
Consequence
COL9A2
NM_001852.4 intron
NM_001852.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.20
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=-0.83).
BP6
?
Variant 1-40314169-G-T is Benign according to our data. Variant chr1-40314169-G-T is described in ClinVar as [Benign]. Clinvar id is 258384.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL9A2 | NM_001852.4 | c.249+36C>A | intron_variant | ENST00000372748.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL9A2 | ENST00000372748.8 | c.249+36C>A | intron_variant | 1 | NM_001852.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.106 AC: 16136AN: 152020Hom.: 1227 Cov.: 32
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GnomAD3 exomes AF: 0.0879 AC: 22101AN: 251302Hom.: 1405 AF XY: 0.0858 AC XY: 11659AN XY: 135824
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GnomAD4 exome AF: 0.0625 AC: 91204AN: 1458818Hom.: 4202 Cov.: 32 AF XY: 0.0641 AC XY: 46524AN XY: 725900
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GnomAD4 genome ? AF: 0.106 AC: 16172AN: 152138Hom.: 1239 Cov.: 32 AF XY: 0.108 AC XY: 8036AN XY: 74406
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 26, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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