20-63307491-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2
The ENST00000358894.11(COL20A1):c.498C>T(p.Ala166=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000358 in 1,610,752 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
ENST00000358894.11 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL20A1 | NM_020882.4 | c.498C>T | p.Ala166= | splice_region_variant, synonymous_variant | 6/36 | ENST00000358894.11 | NP_065933.2 | |
COL20A1 | XM_011528937.2 | c.498C>T | p.Ala166= | splice_region_variant, synonymous_variant | 6/36 | XP_011527239.1 | ||
COL20A1 | XM_011528938.2 | c.498C>T | p.Ala166= | splice_region_variant, synonymous_variant | 6/36 | XP_011527240.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL20A1 | ENST00000358894.11 | c.498C>T | p.Ala166= | splice_region_variant, synonymous_variant | 6/36 | 1 | NM_020882.4 | ENSP00000351767 | P2 | |
COL20A1 | ENST00000479501.5 | n.560C>T | splice_region_variant, non_coding_transcript_exon_variant | 6/36 | 1 | |||||
COL20A1 | ENST00000422202.5 | c.519C>T | p.Thr173= | splice_region_variant, synonymous_variant | 5/35 | 5 | ENSP00000414753 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000361 AC: 55AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000449 AC: 110AN: 244806Hom.: 1 AF XY: 0.000516 AC XY: 69AN XY: 133618
GnomAD4 exome AF: 0.000358 AC: 522AN: 1458430Hom.: 3 Cov.: 32 AF XY: 0.000398 AC XY: 289AN XY: 725544
GnomAD4 genome AF: 0.000361 AC: 55AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.000376 AC XY: 28AN XY: 74482
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at