chr12-47985773-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM1PM2PP2BP4
The NM_001844.5(COL2A1):c.1635C>A(p.Asn545Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N545S) has been classified as Likely benign.
Frequency
Consequence
NM_001844.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COL2A1 | NM_001844.5 | c.1635C>A | p.Asn545Lys | missense_variant | 25/54 | ENST00000380518.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COL2A1 | ENST00000380518.8 | c.1635C>A | p.Asn545Lys | missense_variant | 25/54 | 1 | NM_001844.5 | P1 | |
COL2A1 | ENST00000337299.7 | c.1428C>A | p.Asn476Lys | missense_variant | 24/53 | 1 | |||
COL2A1 | ENST00000493991.5 | n.559C>A | non_coding_transcript_exon_variant | 8/37 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249234Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134868
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461446Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727002
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at