Variant rs1903787 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.2656-28T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,613,396 control chromosomes in the GnomAD database, including 61,716 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8671 hom., cov: 32)

Exomes 𝑓: 0.26 ( 53045 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.507

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 1-102978941-A-G is Benign according to our data. Variant chr1-102978941-A-G is described in ClinVar as [Benign]. Clinvar id is 258449.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL11A1	NM_001854.4 linkuse as main transcript	c.2656-28T>C		intron_variant		ENST00000370096.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL11A1	ENST00000370096.9 linkuse as main transcript	c.2656-28T>C		intron_variant		1	NM_001854.4	P1	P12107-1

Frequencies

GnomAD3 genomes

AF:

0.317

AC:

48191

AN:

151922

Hom.:

8652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.499

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.263

Gnomad ASJ

AF:

0.221

Gnomad EAS

AF:

0.0865

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.316

Gnomad NFE

AF:

0.263

Gnomad OTH

AF:

0.282

GnomAD3 exomes

AF:

0.257

AC:

64600

AN:

250996

Hom.:

9163

AF XY:

0.249

AC XY:

33822

AN XY:

135662

show subpopulations

Gnomad AFR exome

AF:

0.508

Gnomad AMR exome

AF:

0.276

Gnomad ASJ exome

AF:

0.230

Gnomad EAS exome

AF:

0.0886

Gnomad SAS exome

AF:

0.164

Gnomad FIN exome

AF:

0.272

Gnomad NFE exome

AF:

0.268

Gnomad OTH exome

AF:

0.258

GnomAD4 exome

AF:

0.263

AC:

384508

AN:

1461356

Hom.:

53045

Cov.:

AF XY:

0.260

AC XY:

188862

AN XY:

727002

show subpopulations

Gnomad4 AFR exome

AF:

0.507

Gnomad4 AMR exome

AF:

0.277

Gnomad4 ASJ exome

AF:

0.231

Gnomad4 EAS exome

AF:

0.0749

Gnomad4 SAS exome

AF:

0.168

Gnomad4 FIN exome

AF:

0.272

Gnomad4 NFE exome

AF:

0.269

Gnomad4 OTH exome

AF:

0.267

GnomAD4 genome

AF:

0.317

AC:

48263

AN:

152040

Hom.:

8671

Cov.:

AF XY:

0.313

AC XY:

23296

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.500

Gnomad4 AMR

AF:

0.263

Gnomad4 ASJ

AF:

0.221

Gnomad4 EAS

AF:

0.0865

Gnomad4 SAS

AF:

0.162

Gnomad4 FIN

AF:

0.271

Gnomad4 NFE

AF:

0.263

Gnomad4 OTH

AF:

0.281

Alfa

AF:

0.276

Hom.:

6330

Bravo

AF:

0.326

Asia WGS

AF:

0.174

AC:

605

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hearing loss, autosomal dominant 37

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 22, 2021

- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

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

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 23, 2018

- -

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

1.0

DANN

Benign

0.38

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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