20-63306030-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020882.4(COL20A1):c.487C>T(p.Arg163Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000298 in 1,610,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020882.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL20A1 | NM_020882.4 | c.487C>T | p.Arg163Cys | missense_variant | Exon 5 of 36 | ENST00000358894.11 | NP_065933.2 | |
COL20A1 | XM_011528937.2 | c.487C>T | p.Arg163Cys | missense_variant | Exon 5 of 36 | XP_011527239.1 | ||
COL20A1 | XM_011528938.2 | c.487C>T | p.Arg163Cys | missense_variant | Exon 5 of 36 | XP_011527240.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL20A1 | ENST00000358894.11 | c.487C>T | p.Arg163Cys | missense_variant | Exon 5 of 36 | 1 | NM_020882.4 | ENSP00000351767.6 | ||
COL20A1 | ENST00000479501.5 | n.549C>T | non_coding_transcript_exon_variant | Exon 5 of 36 | 1 | |||||
COL20A1 | ENST00000422202.5 | c.487C>T | p.Arg163Cys | missense_variant | Exon 4 of 35 | 5 | ENSP00000414753.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152254Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000408 AC: 10AN: 245194Hom.: 0 AF XY: 0.0000375 AC XY: 5AN XY: 133248
GnomAD4 exome AF: 0.0000309 AC: 45AN: 1458026Hom.: 0 Cov.: 32 AF XY: 0.0000317 AC XY: 23AN XY: 725136
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152254Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.487C>T (p.R163C) alteration is located in exon 5 (coding exon 4) of the COL20A1 gene. This alteration results from a C to T substitution at nucleotide position 487, causing the arginine (R) at amino acid position 163 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at