Genetic Variant COL11A1:c.1792-12_1792-10delATG (chr1-103005900-CCAT-C) – ACMG Classification: Benign (-16 pts)

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001854.4(COL11A1):c.1792-12_1792-10delATG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.77 in 1,517,264 control chromosomes in the GnomAD database, including 434,303 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.77 ( 46376 hom., cov: 0)

Exomes 𝑓: 0.77 ( 387927 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Not classified

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 2.23

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 -16 ACMG points.

BP6

Variant 1-103005900-CCAT-C is Benign according to our data. Variant chr1-103005900-CCAT-C is described in ClinVar as [Likely_benign]. Clinvar id is 93966.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-103005900-CCAT-C is described in Lovd as [Benign]. Variant chr1-103005900-CCAT-C is described in Lovd as [Benign]. Variant chr1-103005900-CCAT-C is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A1	NM_001854.4 link	c.1792-12_1792-10delATG		intron_variant	Intron 17 of 66	ENST00000370096.9	NP_001845.3	P12107-1Q59HB5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COL11A1	ENST00000370096.9 link	c.1792-12_1792-10delATG		intron_variant	Intron 17 of 66	1	NM_001854.4	ENSP00000359114.3		P12107-1

Frequencies

GnomAD3 genomes

AF:

0.775

AC:

116445

AN:

150312

Hom.:

46344

Cov.:

show subpopulations

Gnomad AFR

AF:

0.571

Gnomad AMI

AF:

0.733

Gnomad AMR

AF:

0.871

Gnomad ASJ

AF:

0.761

Gnomad EAS

AF:

0.994

Gnomad SAS

AF:

0.869

Gnomad FIN

AF:

0.812

Gnomad MID

AF:

0.848

Gnomad NFE

AF:

0.848

Gnomad OTH

AF:

0.792

GnomAD3 exomes

AF:

0.804

AC:

157046

AN:

195300

Hom.:

63280

AF XY:

0.806

AC XY:

84689

AN XY:

105128

show subpopulations

Gnomad AFR exome

AF:

0.525

Gnomad AMR exome

AF:

0.896

Gnomad ASJ exome

AF:

0.706

Gnomad EAS exome

AF:

0.992

Gnomad SAS exome

AF:

0.814

Gnomad FIN exome

AF:

0.799

Gnomad NFE exome

AF:

0.804

Gnomad OTH exome

AF:

0.794

GnomAD4 exome

AF:

0.770

AC:

1052443

AN:

1366840

Hom.:

387927

AF XY:

0.770

AC XY:

524328

AN XY:

680926

show subpopulations

Gnomad4 AFR exome

AF:

0.520

Gnomad4 AMR exome

AF:

0.825

Gnomad4 ASJ exome

AF:

0.685

Gnomad4 EAS exome

AF:

0.890

Gnomad4 SAS exome

AF:

0.761

Gnomad4 FIN exome

AF:

0.763

Gnomad4 NFE exome

AF:

0.775

Gnomad4 OTH exome

AF:

0.756

GnomAD4 genome

AF:

0.775

AC:

116528

AN:

150424

Hom.:

46376

Cov.:

AF XY:

0.777

AC XY:

56958

AN XY:

73338

show subpopulations

Gnomad4 AFR

AF:

0.571

Gnomad4 AMR

AF:

0.872

Gnomad4 ASJ

AF:

0.761

Gnomad4 EAS

AF:

0.994

Gnomad4 SAS

AF:

0.869

Gnomad4 FIN

AF:

0.812

Gnomad4 NFE

AF:

0.848

Gnomad4 OTH

AF:

0.794

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

May 05, 2014

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 29, 2016

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Frequency -

not provided

Benign:2

Sep 30, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Hearing loss, autosomal dominant 37

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Marshall syndrome

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Fibrochondrogenesis 1

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Stickler syndrome type 2

Benign:1

Jul 22, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

1-103005900-CCATCATCATCATCATCAT-CCATCATCATCATCAT

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