chr20-62817581-C-A
Variant summary
Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001853.4(COL9A3):c.93C>A(p.Pro31Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0811 in 1,539,566 control chromosomes in the GnomAD database, including 6,673 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001853.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- epiphyseal dysplasia, multiple, 3Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Illumina, G2P, Labcorp Genetics (formerly Invitae)
- Stickler syndromeInheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Ambry Genetics, Genomics England PanelApp, ClinGen
- Stickler syndrome, type 6Inheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
- multiple epiphyseal dysplasia due to collagen 9 anomalyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- autosomal recessive Stickler syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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COL9A3 | ENST00000649368.1 | c.93C>A | p.Pro31Pro | synonymous_variant | Exon 2 of 32 | NM_001853.4 | ENSP00000496793.1 | |||
COL9A3 | ENST00000477612.5 | n.89C>A | non_coding_transcript_exon_variant | Exon 2 of 12 | 3 | |||||
COL9A3 | ENST00000489045.5 | n.139C>A | non_coding_transcript_exon_variant | Exon 1 of 14 | 5 | |||||
COL9A3 | ENST00000452372.2 | c.-253C>A | upstream_gene_variant | 5 | ENSP00000394280.1 |
Frequencies
GnomAD3 genomes AF: 0.116 AC: 17559AN: 151698Hom.: 1248 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.110 AC: 15857AN: 143678 AF XY: 0.106 show subpopulations
GnomAD4 exome AF: 0.0773 AC: 107298AN: 1387750Hom.: 5421 Cov.: 30 AF XY: 0.0774 AC XY: 52982AN XY: 684142 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.116 AC: 17601AN: 151816Hom.: 1252 Cov.: 33 AF XY: 0.117 AC XY: 8709AN XY: 74184 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not specified Benign:3
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. -
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not provided Benign:3
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Epiphyseal dysplasia, multiple, 3 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at