rs143930593
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001853.4(COL9A3):āc.1485C>Gā(p.Pro495=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,830 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 Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. P495P) has been classified as Likely benign.
Frequency
Consequence
NM_001853.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL9A3 | NM_001853.4 | c.1485C>G | p.Pro495= | synonymous_variant | 28/32 | ENST00000649368.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL9A3 | ENST00000649368.1 | c.1485C>G | p.Pro495= | synonymous_variant | 28/32 | NM_001853.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152244Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000201 AC: 5AN: 248848Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135346
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461468Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 727058
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152362Hom.: 0 Cov.: 34 AF XY: 0.0000268 AC XY: 2AN XY: 74502
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at