rs1983658
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001852.4(COL9A2):c.303+26G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000281 in 1,567,286 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00034 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00028 ( 3 hom. )
Consequence
COL9A2
NM_001852.4 intron
NM_001852.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.02
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 1-40312705-C-G is Benign according to our data. Variant chr1-40312705-C-G is described in ClinVar as [Likely_benign]. Clinvar id is 1213166.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.000335 (51/152122) while in subpopulation AMR AF= 0.00294 (45/15286). AF 95% confidence interval is 0.00226. There are 0 homozygotes in gnomad4. There are 23 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAdExome4 at 3 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL9A2 | NM_001852.4 | c.303+26G>C | intron_variant | ENST00000372748.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL9A2 | ENST00000372748.8 | c.303+26G>C | intron_variant | 1 | NM_001852.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000336 AC: 51AN: 152004Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00180 AC: 315AN: 175218Hom.: 3 AF XY: 0.00140 AC XY: 131AN XY: 93304
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GnomAD4 exome AF: 0.000276 AC: 390AN: 1415164Hom.: 3 Cov.: 34 AF XY: 0.000239 AC XY: 167AN XY: 699890
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GnomAD4 genome ? AF: 0.000335 AC: 51AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.000309 AC XY: 23AN XY: 74356
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 15, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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