rs143848379
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_001851.6(COL9A1):c.353G>A(p.Arg118Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000167 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001851.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL9A1 | NM_001851.6 | c.353G>A | p.Arg118Gln | missense_variant | Exon 5 of 38 | ENST00000357250.11 | NP_001842.3 | |
COL9A1 | NM_001377291.1 | c.353G>A | p.Arg118Gln | missense_variant | Exon 5 of 11 | NP_001364220.1 | ||
COL9A1 | XM_011535429.4 | c.353G>A | p.Arg118Gln | missense_variant | Exon 5 of 39 | XP_011533731.1 | ||
COL9A1 | XM_017010246.3 | c.-12-185G>A | intron_variant | Intron 1 of 35 | XP_016865735.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL9A1 | ENST00000357250.11 | c.353G>A | p.Arg118Gln | missense_variant | Exon 5 of 38 | 1 | NM_001851.6 | ENSP00000349790.6 | ||
COL9A1 | ENST00000370496.3 | c.353G>A | p.Arg118Gln | missense_variant | Exon 5 of 11 | 1 | ENSP00000359527.3 |
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000175 AC: 44AN: 250800Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135566
GnomAD4 exome AF: 0.000126 AC: 184AN: 1461760Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 78AN XY: 727188
GnomAD4 genome AF: 0.000565 AC: 86AN: 152274Hom.: 0 Cov.: 32 AF XY: 0.000604 AC XY: 45AN XY: 74476
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function -
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Epiphyseal dysplasia, multiple, 6;C3279941:Stickler syndrome, type 4 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at