NM_001852.4:c.738+10T>C
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001852.4(COL9A2):c.738+10T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0533 in 1,613,950 control chromosomes in the GnomAD database, including 2,581 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001852.4 intron
Scores
Clinical Significance
Conservation
Publications
- epiphyseal dysplasia, multiple, 2Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- Stickler syndrome, type 5Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, PanelApp Australia, Labcorp Genetics (formerly Invitae), Ambry Genetics, Genomics England PanelApp
- multiple epiphyseal dysplasia due to collagen 9 anomalyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- autosomal recessive Stickler syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Stickler syndromeInheritance: AR Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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COL9A2 | ENST00000372748.8 | c.738+10T>C | intron_variant | Intron 14 of 31 | 1 | NM_001852.4 | ENSP00000361834.3 | |||
COL9A2 | ENST00000482722.5 | n.1041+10T>C | intron_variant | Intron 13 of 30 | 1 | |||||
COL9A2 | ENST00000488463.6 | n.789+10T>C | intron_variant | Intron 13 of 13 | 5 | |||||
COL9A2 | ENST00000417105.6 | c.*36T>C | downstream_gene_variant | 5 | ENSP00000388493.2 |
Frequencies
GnomAD3 genomes AF: 0.0426 AC: 6481AN: 152114Hom.: 217 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0444 AC: 11170AN: 251408 AF XY: 0.0458 show subpopulations
GnomAD4 exome AF: 0.0544 AC: 79587AN: 1461718Hom.: 2364 Cov.: 34 AF XY: 0.0542 AC XY: 39403AN XY: 727172 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0426 AC: 6480AN: 152232Hom.: 217 Cov.: 32 AF XY: 0.0429 AC XY: 3191AN XY: 74424 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:4
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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. -
not provided Benign:2
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Epiphyseal dysplasia, multiple, 2 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Connective tissue disorder Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at