Variant rs34587338 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_001854.4(COL11A1):c.1308+19A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0636 in 1,562,682 control chromosomes in the GnomAD database, including 3,450 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.079 ( 531 hom., cov: 30)

Exomes 𝑓: 0.062 ( 2919 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 0.0400

Variant links:

Genes affected

COL11A1 (HGNC:2186): (collagen type XI alpha 1 chain) This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Mutations in this gene are associated with type II Stickler syndrome and with Marshall syndrome. A single-nucleotide polymorphism in this gene is also associated with susceptibility to lumbar disc herniation. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]

COL11A1 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=-0.83).

BP6

Variant 1-103021688-T-C is Benign according to our data. Variant chr1-103021688-T-C is described in ClinVar as [Benign]. Clinvar id is 93965.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-103021688-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.111 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COL11A1	NM_001854.4 linkuse as main transcript	c.1308+19A>G		intron_variant		ENST00000370096.9	NP_001845.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COL11A1	ENST00000370096.9 linkuse as main transcript	c.1308+19A>G		intron_variant		1	NM_001854.4	ENSP00000359114	P1	P12107-1

Frequencies

GnomAD3 genomes

AF:

0.0789

AC:

11992

AN:

151992

Hom.:

528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.0662

Gnomad ASJ

AF:

0.0730

Gnomad EAS

AF:

0.0721

Gnomad SAS

AF:

0.0722

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.0591

Gnomad OTH

AF:

0.0789

GnomAD3 exomes

AF:

0.0706

AC:

17752

AN:

251340

Hom.:

717

AF XY:

0.0704

AC XY:

9562

AN XY:

135842

show subpopulations

Gnomad AFR exome

AF:

0.115

Gnomad AMR exome

AF:

0.0545

Gnomad ASJ exome

AF:

0.0822

Gnomad EAS exome

AF:

0.0797

Gnomad SAS exome

AF:

0.0680

Gnomad FIN exome

AF:

0.101

Gnomad NFE exome

AF:

0.0615

Gnomad OTH exome

AF:

0.0705

GnomAD4 exome

AF:

0.0619

AC:

87313

AN:

1410572

Hom.:

2919

Cov.:

AF XY:

0.0621

AC XY:

43786

AN XY:

705182

show subpopulations

Gnomad4 AFR exome

AF:

0.118

Gnomad4 AMR exome

AF:

0.0555

Gnomad4 ASJ exome

AF:

0.0792

Gnomad4 EAS exome

AF:

0.0638

Gnomad4 SAS exome

AF:

0.0671

Gnomad4 FIN exome

AF:

0.0994

Gnomad4 NFE exome

AF:

0.0571

Gnomad4 OTH exome

AF:

0.0691

GnomAD4 genome

AF:

0.0790

AC:

12023

AN:

152110

Hom.:

531

Cov.:

AF XY:

0.0803

AC XY:

5975

AN XY:

74388

show subpopulations

Gnomad4 AFR

AF:

0.114

Gnomad4 AMR

AF:

0.0661

Gnomad4 ASJ

AF:

0.0730

Gnomad4 EAS

AF:

0.0723

Gnomad4 SAS

AF:

0.0725

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.0591

Gnomad4 OTH

AF:

0.0785

Alfa

AF:

0.0705

Hom.:

Bravo

AF:

0.0793

Asia WGS

AF:

0.0690

AC:

238

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Sep 26, 2013	- -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Oct 04, 2016	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 provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

4.1

DANN

Benign

0.44

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