Variant chr20-62827195-A-T 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_001853.4(COL9A3):c.793-46A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 1,605,714 control chromosomes in the GnomAD database, including 192,344 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 25897 hom., cov: 32)

Exomes 𝑓: 0.47 ( 166447 hom. )

Consequence

COL9A3
NM_001853.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.84

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:

COL9A3 (HGNC:):

COL9A3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP6

Variant 20-62827195-A-T is Benign according to our data. Variant chr20-62827195-A-T is described in ClinVar as [Benign]. Clinvar id is 258434.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL9A3	NM_001853.4 linkuse as main transcript	c.793-46A>T		intron_variant		ENST00000649368.1	NP_001844.3	Q14050

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL9A3	ENST00000649368.1 linkuse as main transcript	c.793-46A>T		intron_variant			NM_001853.4	ENSP00000496793.1		Q14050
COL9A3	ENST00000463487.2 linkuse as main transcript	n.501-46A>T		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.562

AC:

85226

AN:

151740

Hom.:

25833

Cov.:

show subpopulations

Gnomad AFR

AF:

0.796

Gnomad AMI

AF:

0.307

Gnomad AMR

AF:

0.514

Gnomad ASJ

AF:

0.467

Gnomad EAS

AF:

0.757

Gnomad SAS

AF:

0.549

Gnomad FIN

AF:

0.469

Gnomad MID

AF:

0.535

Gnomad NFE

AF:

0.439

Gnomad OTH

AF:

0.545

GnomAD3 exomes

AF:

0.518

AC:

128969

AN:

248812

Hom.:

35082

AF XY:

0.509

AC XY:

68787

AN XY:

135112

show subpopulations

Gnomad AFR exome

AF:

0.805

Gnomad AMR exome

AF:

0.543

Gnomad ASJ exome

AF:

0.447

Gnomad EAS exome

AF:

0.761

Gnomad SAS exome

AF:

0.536

Gnomad FIN exome

AF:

0.472

Gnomad NFE exome

AF:

0.442

Gnomad OTH exome

AF:

0.487

GnomAD4 exome

AF:

0.471

AC:

685381

AN:

1453856

Hom.:

166447

Cov.:

AF XY:

0.472

AC XY:

341501

AN XY:

723732

show subpopulations

Gnomad4 AFR exome

AF:

0.813

Gnomad4 AMR exome

AF:

0.541

Gnomad4 ASJ exome

AF:

0.452

Gnomad4 EAS exome

AF:

0.750

Gnomad4 SAS exome

AF:

0.535

Gnomad4 FIN exome

AF:

0.463

Gnomad4 NFE exome

AF:

0.442

Gnomad4 OTH exome

AF:

0.499

GnomAD4 genome

AF:

0.562

AC:

85351

AN:

151858

Hom.:

25897

Cov.:

AF XY:

0.561

AC XY:

41624

AN XY:

74198

show subpopulations

Gnomad4 AFR

AF:

0.796

Gnomad4 AMR

AF:

0.514

Gnomad4 ASJ

AF:

0.467

Gnomad4 EAS

AF:

0.757

Gnomad4 SAS

AF:

0.549

Gnomad4 FIN

AF:

0.469

Gnomad4 NFE

AF:

0.439

Gnomad4 OTH

AF:

0.551

Alfa

AF:

0.485

Hom.:

3342

Bravo

AF:

0.577

Asia WGS

AF:

0.657

AC:

2284

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	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 16, 2018	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

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

-0.94

CADD

Benign

0.12

DANN

Benign

0.50

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