Genetic Variant COL20A1:p.Thr141Thr (chr20-63305966-G-A) – ACMG Classification: Benign (-17 pts)

Variant summary

Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2

The NM_020882.4(COL20A1):c.423G>A(p.Thr141Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0102 in 1,612,624 control chromosomes in the GnomAD database, including 125 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0070 ( 8 hom., cov: 31)

Exomes 𝑓: 0.011 ( 117 hom. )

Consequence

COL20A1
NM_020882.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.05

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]

COL20A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -17 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BP6

Variant 20-63305966-G-A is Benign according to our data. Variant chr20-63305966-G-A is described in ClinVar as [Benign]. Clinvar id is 787606.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=1.05 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL20A1	NM_020882.4 link	c.423G>A	p.Thr141Thr	synonymous_variant	Exon 5 of 36	ENST00000358894.11	NP_065933.2	Q9P218-1
COL20A1	XM_011528937.2 link	c.423G>A	p.Thr141Thr	synonymous_variant	Exon 5 of 36		XP_011527239.1
COL20A1	XM_011528938.2 link	c.423G>A	p.Thr141Thr	synonymous_variant	Exon 5 of 36		XP_011527240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
COL20A1	ENST00000358894.11 link	c.423G>A	p.Thr141Thr	synonymous_variant	Exon 5 of 36	1	NM_020882.4	ENSP00000351767.6	Q9P218-1
COL20A1	ENST00000479501.5 link	n.485G>A		non_coding_transcript_exon_variant	Exon 5 of 36	1
COL20A1	ENST00000422202.5 link	c.423G>A	p.Thr141Thr	synonymous_variant	Exon 4 of 35	5		ENSP00000414753.1	Q9P218-2

Frequencies

GnomAD3 genomes

AF:

0.00698

AC:

1062

AN:

152188

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00212

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00393

Gnomad ASJ

AF:

0.00259

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.00612

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0120

Gnomad OTH

AF:

0.00574

GnomAD3 exomes

AF:

0.00725

AC:

1794

AN:

247410

Hom.:

AF XY:

0.00739

AC XY:

996

AN XY:

134698

show subpopulations

Gnomad AFR exome

AF:

0.00267

Gnomad AMR exome

AF:

0.00378

Gnomad ASJ exome

AF:

0.00261

Gnomad EAS exome

AF:

0.0000557

Gnomad SAS exome

AF:

0.00268

Gnomad FIN exome

AF:

0.00596

Gnomad NFE exome

AF:

0.0120

Gnomad OTH exome

AF:

0.00683

GnomAD4 exome

AF:

0.0106

AC:

15456

AN:

1460318

Hom.:

117

Cov.:

AF XY:

0.0103

AC XY:

7512

AN XY:

726444

show subpopulations

Gnomad4 AFR exome

AF:

0.00155

Gnomad4 AMR exome

AF:

0.00412

Gnomad4 ASJ exome

AF:

0.00283

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00234

Gnomad4 FIN exome

AF:

0.00558

Gnomad4 NFE exome

AF:

0.0127

Gnomad4 OTH exome

AF:

0.00833

GnomAD4 genome

AF:

0.00696

AC:

1060

AN:

152306

Hom.:

Cov.:

AF XY:

0.00648

AC XY:

483

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.00209

Gnomad4 AMR

AF:

0.00392

Gnomad4 ASJ

AF:

0.00259

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00269

Gnomad4 FIN

AF:

0.00612

Gnomad4 NFE

AF:

0.0120

Gnomad4 OTH

AF:

0.00568

Alfa

AF:

0.00902

Hom.:

Bravo

AF:

0.00667

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.0118

EpiControl

AF:

0.0108

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jul 21, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.3

DANN

Benign

0.70

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over