chr20-62824439-C-T

Position:

chr20-62824439-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_001853.4(COL9A3):c.520-6C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 1,599,674 control chromosomes in the GnomAD database, including 212 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0090 ( 12 hom., cov: 33)

Exomes 𝑓: 0.014 ( 200 hom. )

Consequence

COL9A3
NM_001853.4 splice_region, splice_polypyrimidine_tract, intron

Scores

Splicing: ADA: 0.0003695

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: -0.647

Variant links:

Genes affected

COL9A3 (HGNC:2219): (collagen type IX alpha 3 chain) This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]

COL9A3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.62).

BP6

Variant 20-62824439-C-T is Benign according to our data. Variant chr20-62824439-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 258426.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr20-62824439-C-T is described in Lovd as [Likely_benign]. Variant chr20-62824439-C-T is described in Lovd as [Benign].

BS1

Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.00905 (1378/152272) while in subpopulation SAS AF= 0.0263 (127/4828). AF 95% confidence interval is 0.0226. There are 12 homozygotes in gnomad4. There are 620 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 12 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL9A3	NM_001853.4 linkuse as main transcript	c.520-6C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000649368.1	NP_001844.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL9A3	ENST00000649368.1 linkuse as main transcript	c.520-6C>T		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant			NM_001853.4	ENSP00000496793	P1

Frequencies

GnomAD3 genomes

AF:

0.00906

AC:

1379

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00249

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00301

Gnomad ASJ

AF:

0.00432

Gnomad EAS

AF:

0.0226

Gnomad SAS

AF:

0.0265

Gnomad FIN

AF:

0.00226

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.0137

Gnomad OTH

AF:

0.00478

GnomAD3 exomes

AF:

0.0111

AC:

2512

AN:

225928

Hom.:

AF XY:

0.0123

AC XY:

1512

AN XY:

122546

show subpopulations

Gnomad AFR exome

AF:

0.00115

Gnomad AMR exome

AF:

0.00279

Gnomad ASJ exome

AF:

0.00188

Gnomad EAS exome

AF:

0.0206

Gnomad SAS exome

AF:

0.0252

Gnomad FIN exome

AF:

0.00191

Gnomad NFE exome

AF:

0.0125

Gnomad OTH exome

AF:

0.00588

GnomAD4 exome

AF:

0.0139

AC:

20138

AN:

1447402

Hom.:

200

Cov.:

AF XY:

0.0143

AC XY:

10271

AN XY:

718848

show subpopulations

Gnomad4 AFR exome

AF:

0.00180

Gnomad4 AMR exome

AF:

0.00283

Gnomad4 ASJ exome

AF:

0.00286

Gnomad4 EAS exome

AF:

0.0188

Gnomad4 SAS exome

AF:

0.0253

Gnomad4 FIN exome

AF:

0.00301

Gnomad4 NFE exome

AF:

0.0146

Gnomad4 OTH exome

AF:

0.0110

GnomAD4 genome

AF:

0.00905

AC:

1378

AN:

152272

Hom.:

Cov.:

AF XY:

0.00833

AC XY:

620

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.00248

Gnomad4 AMR

AF:

0.00301

Gnomad4 ASJ

AF:

0.00432

Gnomad4 EAS

AF:

0.0228

Gnomad4 SAS

AF:

0.0263

Gnomad4 FIN

AF:

0.00226

Gnomad4 NFE

AF:

0.0137

Gnomad4 OTH

AF:

0.00473

Alfa

AF:

0.0105

Hom.:

Bravo

AF:

0.00815

Asia WGS

AF:

0.0250

AC:

AN:

3478

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:4

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 30, 2020	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Aug 06, 2020	- -

Intervertebral disc disorder;C1832998:Epiphyseal dysplasia, multiple, 3

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Aug 12, 2021

- -

Connective tissue disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Mar 11, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.93

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.00037

dbscSNV1_RF

Benign

0.022

SpliceAI score (max)

0.19

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