20-63307997-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_020882.4(COL20A1):​c.682C>T​(p.Gln228*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 33)

Consequence

COL20A1
NM_020882.4 stop_gained

Scores

2
2
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.231
Variant links:
Genes affected
COL20A1 (HGNC:14670): (collagen type XX alpha 1 chain) Predicted to be located in endoplasmic reticulum lumen and extracellular region. Predicted to be part of collagen trimer. Predicted to be active in collagen-containing extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COL20A1NM_020882.4 linkc.682C>T p.Gln228* stop_gained Exon 7 of 36 ENST00000358894.11 NP_065933.2 Q9P218-1
COL20A1XM_011528937.2 linkc.682C>T p.Gln228* stop_gained Exon 7 of 36 XP_011527239.1
COL20A1XM_011528938.2 linkc.682C>T p.Gln228* stop_gained Exon 7 of 36 XP_011527240.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COL20A1ENST00000358894.11 linkc.682C>T p.Gln228* stop_gained Exon 7 of 36 1 NM_020882.4 ENSP00000351767.6 Q9P218-1
COL20A1ENST00000479501.5 linkn.744C>T non_coding_transcript_exon_variant Exon 7 of 36 1
COL20A1ENST00000422202.5 linkc.703C>T p.Gln235* stop_gained Exon 6 of 35 5 ENSP00000414753.1 Q9P218-2

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.52
D
BayesDel_noAF
Pathogenic
0.51
CADD
Pathogenic
35
DANN
Uncertain
1.0
Eigen
Uncertain
0.32
Eigen_PC
Benign
0.012
FATHMM_MKL
Benign
0.31
N
Vest4
0.17
GERP RS
3.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.11
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-61939349; API