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:

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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.

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