Variant chr1-102888872-A-G 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 ENST00000370096.9(COL11A1):c.4512T>C(p.Gly1504=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.746 in 1,611,910 control chromosomes in the GnomAD database, including 457,887 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.65 ( 35478 hom., cov: 32)

Exomes 𝑓: 0.76 ( 422409 hom. )

Consequence

COL11A1
ENST00000370096.9 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:13

Conservation

PhyloP100: 0.219

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=-0.5).

BP6

Variant 1-102888872-A-G is Benign according to our data. Variant chr1-102888872-A-G is described in ClinVar as [Benign]. Clinvar id is 258466.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-102888872-A-G is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.783 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.4512T>C	p.Gly1504=	synonymous_variant	60/67	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.4512T>C	p.Gly1504=	synonymous_variant	60/67	1	NM_001854.4	ENSP00000359114	P1	P12107-1

Frequencies

GnomAD3 genomes

AF:

0.651

AC:

98840

AN:

151896

Hom.:

35469

Cov.:

show subpopulations

Gnomad AFR

AF:

0.315

Gnomad AMI

AF:

0.780

Gnomad AMR

AF:

0.795

Gnomad ASJ

AF:

0.803

Gnomad EAS

AF:

0.742

Gnomad SAS

AF:

0.645

Gnomad FIN

AF:

0.806

Gnomad MID

AF:

0.804

Gnomad NFE

AF:

0.780

Gnomad OTH

AF:

0.712

GnomAD3 exomes

AF:

0.737

AC:

184970

AN:

251086

Hom.:

70321

AF XY:

0.739

AC XY:

100325

AN XY:

135710

show subpopulations

Gnomad AFR exome

AF:

0.304

Gnomad AMR exome

AF:

0.825

Gnomad ASJ exome

AF:

0.794

Gnomad EAS exome

AF:

0.720

Gnomad SAS exome

AF:

0.649

Gnomad FIN exome

AF:

0.808

Gnomad NFE exome

AF:

0.777

Gnomad OTH exome

AF:

0.774

GnomAD4 exome

AF:

0.756

AC:

1103516

AN:

1459896

Hom.:

422409

Cov.:

AF XY:

0.755

AC XY:

548116

AN XY:

726384

show subpopulations

Gnomad4 AFR exome

AF:

0.293

Gnomad4 AMR exome

AF:

0.822

Gnomad4 ASJ exome

AF:

0.796

Gnomad4 EAS exome

AF:

0.699

Gnomad4 SAS exome

AF:

0.653

Gnomad4 FIN exome

AF:

0.804

Gnomad4 NFE exome

AF:

0.774

Gnomad4 OTH exome

AF:

0.744

GnomAD4 genome

AF:

0.650

AC:

98867

AN:

152014

Hom.:

35478

Cov.:

AF XY:

0.655

AC XY:

48665

AN XY:

74294

show subpopulations

Gnomad4 AFR

AF:

0.314

Gnomad4 AMR

AF:

0.795

Gnomad4 ASJ

AF:

0.803

Gnomad4 EAS

AF:

0.742

Gnomad4 SAS

AF:

0.645

Gnomad4 FIN

AF:

0.806

Gnomad4 NFE

AF:

0.780

Gnomad4 OTH

AF:

0.715

Alfa

AF:

0.753

Hom.:

58877

Bravo

AF:

0.639

Asia WGS

AF:

0.683

AC:

2374

AN:

3478

EpiCase

AF:

0.781

EpiControl

AF:

0.785

ClinVar

Significance: Benign

Submissions summary: Benign:13

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:5

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Sep 29, 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. -
Benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -

Fibrochondrogenesis 1

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Stickler syndrome type 2

Benign:2

Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 22, 2021	- -

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

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

CADD

Benign

4.3

DANN

Benign

0.79

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