Variant rs1012282 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.3168+41T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,571,308 control chromosomes in the GnomAD database, including 55,383 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6451 hom., cov: 32)

Exomes 𝑓: 0.26 ( 48932 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.49

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:

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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=-0.91).

BP6

Variant 1-102961825-A-G is Benign according to our data. Variant chr1-102961825-A-G is described in ClinVar as [Benign]. Clinvar id is 258456.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.376 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.3168+41T>C		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.3168+41T>C		intron_variant		1	NM_001854.4	ENSP00000359114	P1	P12107-1

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

43023

AN:

152016

Hom.:

6440

Cov.:

show subpopulations

Gnomad AFR

AF:

0.381

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.251

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.0864

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.261

GnomAD3 exomes

AF:

0.248

AC:

60776

AN:

244704

Hom.:

7913

AF XY:

0.243

AC XY:

31976

AN XY:

131740

show subpopulations

Gnomad AFR exome

AF:

0.387

Gnomad AMR exome

AF:

0.271

Gnomad ASJ exome

AF:

0.229

Gnomad EAS exome

AF:

0.0884

Gnomad SAS exome

AF:

0.165

Gnomad FIN exome

AF:

0.272

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.253

GnomAD4 exome

AF:

0.258

AC:

365859

AN:

1419174

Hom.:

48932

Cov.:

AF XY:

0.255

AC XY:

180607

AN XY:

708108

show subpopulations

Gnomad4 AFR exome

AF:

0.386

Gnomad4 AMR exome

AF:

0.272

Gnomad4 ASJ exome

AF:

0.230

Gnomad4 EAS exome

AF:

0.0745

Gnomad4 SAS exome

AF:

0.168

Gnomad4 FIN exome

AF:

0.271

Gnomad4 NFE exome

AF:

0.267

Gnomad4 OTH exome

AF:

0.257

GnomAD4 genome

AF:

0.283

AC:

43081

AN:

152134

Hom.:

6451

Cov.:

AF XY:

0.280

AC XY:

20829

AN XY:

74376

show subpopulations

Gnomad4 AFR

AF:

0.381

Gnomad4 AMR

AF:

0.250

Gnomad4 ASJ

AF:

0.221

Gnomad4 EAS

AF:

0.0864

Gnomad4 SAS

AF:

0.162

Gnomad4 FIN

AF:

0.271

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.260

Alfa

AF:

0.271

Hom.:

6186

Bravo

AF:

0.288

Asia WGS

AF:

0.166

AC:

576

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:7

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 23, 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

- -

Hearing loss, autosomal dominant 37

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Marshall syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Fibrochondrogenesis 1

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Stickler syndrome type 2

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.2

DANN

Benign

0.36

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