Variant rs209916 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001852.4(COL9A2):c.792+24C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00893 in 1,613,922 control chromosomes in the GnomAD database, including 231 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 113 hom., cov: 32)

Exomes 𝑓: 0.0073 ( 118 hom. )

Consequence

COL9A2
NM_001852.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0390

Variant links:

Genes affected

COL9A2 (HGNC:2218): (collagen type IX alpha 2 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. This chain is unusual in that, unlike the other two type IX alpha chains, it contains a covalently attached glycosaminoglycan side chain. Mutations in this gene are associated with multiple epiphyseal dysplasia. [provided by RefSeq, Jul 2008]

COL9A2 links:

COL9A2 (HGNC:):

COL9A2 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=-0.81).

BP6

Variant 1-40310087-G-A is Benign according to our data. Variant chr1-40310087-G-A is described in ClinVar as [Benign]. Clinvar id is 258396.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL9A2	NM_001852.4 linkuse as main transcript	c.792+24C>T		intron_variant		ENST00000372748.8	NP_001843.1	Q14055

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
COL9A2	ENST00000372748.8 linkuse as main transcript	c.792+24C>T	intron_variant	1	NM_001852.4	ENSP00000361834.3	Q14055
COL9A2	ENST00000482722.5 linkuse as main transcript	n.1095+24C>T	intron_variant	1
COL9A2	ENST00000488463.6 linkuse as main transcript	n.*24C>T	downstream_gene_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0243

AC:

3691

AN:

152150

Hom.:

108

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0665

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0105

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.000578

Gnomad SAS

AF:

0.00642

Gnomad FIN

AF:

0.0245

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00606

Gnomad OTH

AF:

0.0187

GnomAD3 exomes

AF:

0.0114

AC:

2860

AN:

251284

Hom.:

AF XY:

0.0102

AC XY:

1384

AN XY:

135816

show subpopulations

Gnomad AFR exome

AF:

0.0649

Gnomad AMR exome

AF:

0.00697

Gnomad ASJ exome

AF:

0.00586

Gnomad EAS exome

AF:

0.000652

Gnomad SAS exome

AF:

0.00523

Gnomad FIN exome

AF:

0.0228

Gnomad NFE exome

AF:

0.00688

Gnomad OTH exome

AF:

0.00929

GnomAD4 exome

AF:

0.00732

AC:

10692

AN:

1461654

Hom.:

118

Cov.:

AF XY:

0.00719

AC XY:

5230

AN XY:

727110

show subpopulations

Gnomad4 AFR exome

AF:

0.0645

Gnomad4 AMR exome

AF:

0.00718

Gnomad4 ASJ exome

AF:

0.00677

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.00495

Gnomad4 FIN exome

AF:

0.0222

Gnomad4 NFE exome

AF:

0.00502

Gnomad4 OTH exome

AF:

0.0124

GnomAD4 genome

AF:

0.0244

AC:

3715

AN:

152268

Hom.:

113

Cov.:

AF XY:

0.0242

AC XY:

1801

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.0668

Gnomad4 AMR

AF:

0.0105

Gnomad4 ASJ

AF:

0.00807

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.00622

Gnomad4 FIN

AF:

0.0245

Gnomad4 NFE

AF:

0.00606

Gnomad4 OTH

AF:

0.0199

Alfa

AF:

0.0135

Hom.:

Bravo

AF:

0.0253

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

0.50

DANN

Benign

0.64

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