20-63307997-C-T

Variant names:

• chr20-63307997-C-T
• NM_020882.4:c.682C>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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.231

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]

ACMG classification

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
COL20A1	NM_020882.4	c.682C>T	p.Gln228*	stop_gained	Exon 7 of 36	ENST00000358894.11	NP_065933.2
COL20A1	XM_011528937.2	c.682C>T	p.Gln228*	stop_gained	Exon 7 of 36		XP_011527239.1
COL20A1	XM_011528938.2	c.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
COL20A1	ENST00000358894.11	c.682C>T	p.Gln228*	stop_gained	Exon 7 of 36	1	NM_020882.4	ENSP00000351767.6
COL20A1	ENST00000479501.5	n.744C>T		non_coding_transcript_exon_variant	Exon 7 of 36	1
COL20A1	ENST00000422202.5	c.703C>T	p.Gln235*	stop_gained	Exon 6 of 35	5		ENSP00000414753.1

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;