Variant 20-63307491-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP7BS2

The NM_020882.4(COL20A1):c.498C>T(p.Ala166Ala) 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

Genomes: 𝑓 0.00036 ( 0 hom., cov: 33)

Exomes 𝑓: 0.00036 ( 3 hom. )

Consequence

COL20A1
NM_020882.4 splice_region, synonymous

Scores

Splicing: ADA: 0.00001184

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.101

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:

COL20A1 (HGNC:):

COL20A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP7

Synonymous conserved (PhyloP=-0.101 with no splicing effect.

BS2

High Homozygotes in GnomAdExome4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL20A1	NM_020882.4 linkuse as main transcript	c.498C>T	p.Ala166Ala	splice_region_variant, synonymous_variant	6/36	ENST00000358894.11	NP_065933.2	Q9P218-1
COL20A1	XM_011528937.2 linkuse as main transcript	c.498C>T	p.Ala166Ala	splice_region_variant, synonymous_variant	6/36		XP_011527239.1
COL20A1	XM_011528938.2 linkuse as main transcript	c.498C>T	p.Ala166Ala	splice_region_variant, synonymous_variant	6/36		XP_011527240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
COL20A1	ENST00000358894.11 linkuse as main transcript	c.498C>T	p.Ala166Ala	splice_region_variant, synonymous_variant	6/36	1	NM_020882.4	ENSP00000351767.6	Q9P218-1
COL20A1	ENST00000479501.5 linkuse as main transcript	n.560C>T		splice_region_variant, non_coding_transcript_exon_variant	6/36	1
COL20A1	ENST00000422202.5 linkuse as main transcript	c.519C>T	p.Thr173Thr	splice_region_variant, synonymous_variant	5/35	5		ENSP00000414753.1	Q9P218-2

Frequencies

GnomAD3 genomes

AF:

0.000361

AC:

AN:

152204

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000241

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0000654

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000471

Gnomad OTH

AF:

0.000956

GnomAD3 exomes

AF:

0.000449

AC:

110

AN:

244806

Hom.:

AF XY:

0.000516

AC XY:

AN XY:

133618

show subpopulations

Gnomad AFR exome

AF:

0.000332

Gnomad AMR exome

AF:

0.0000583

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00207

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000326

Gnomad OTH exome

AF:

0.000674

GnomAD4 exome

AF:

0.000358

AC:

522

AN:

1458430

Hom.:

Cov.:

AF XY:

0.000398

AC XY:

289

AN XY:

725544

show subpopulations

Gnomad4 AFR exome

AF:

0.000209

Gnomad4 AMR exome

AF:

0.0000672

Gnomad4 ASJ exome

AF:

0.0000384

Gnomad4 EAS exome

AF:

0.000151

Gnomad4 SAS exome

AF:

0.00159

Gnomad4 FIN exome

AF:

0.0000388

Gnomad4 NFE exome

AF:

0.000302

Gnomad4 OTH exome

AF:

0.000481

GnomAD4 genome

AF:

0.000361

AC:

AN:

152322

Hom.:

Cov.:

AF XY:

0.000376

AC XY:

AN XY:

74482

show subpopulations

Gnomad4 AFR

AF:

0.000240

Gnomad4 AMR

AF:

0.0000653

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000471

Gnomad4 OTH

AF:

0.000946

Alfa

AF:

0.000144

Hom.:

Bravo

AF:

0.000268

EpiCase

AF:

0.000545

EpiControl

AF:

0.000475

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.6

DANN

Benign

0.51

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000012

dbscSNV1_RF

Benign

0.0

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over