Genetic Variant COL11A1:c.274+42G>C (chr1-103082763-C-G) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001854.4(COL11A1):c.274+42G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.571 in 1,522,820 control chromosomes in the GnomAD database, including 256,878 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.50 ( 20957 hom., cov: 32)

Exomes 𝑓: 0.58 ( 235921 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.0730

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=-0.83).

BP6

Variant 1-103082763-C-G is Benign according to our data. Variant chr1-103082763-C-G is described in ClinVar as [Benign]. Clinvar id is 258450.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A1	NM_001854.4 link	c.274+42G>C		intron_variant	Intron 2 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.274+42G>C		intron_variant	Intron 2 of 66	1	NM_001854.4	ENSP00000359114.3		P12107-1

Frequencies

GnomAD3 genomes

AF:

0.497

AC:

75428

AN:

151636

Hom.:

20948

Cov.:

show subpopulations

Gnomad AFR

AF:

0.247

Gnomad AMI

AF:

0.620

Gnomad AMR

AF:

0.624

Gnomad ASJ

AF:

0.520

Gnomad EAS

AF:

0.909

Gnomad SAS

AF:

0.704

Gnomad FIN

AF:

0.492

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.572

Gnomad OTH

AF:

0.544

GnomAD3 exomes

AF:

0.592

AC:

133320

AN:

225314

Hom.:

41322

AF XY:

0.598

AC XY:

73435

AN XY:

122842

show subpopulations

Gnomad AFR exome

AF:

0.237

Gnomad AMR exome

AF:

0.654

Gnomad ASJ exome

AF:

0.510

Gnomad EAS exome

AF:

0.907

Gnomad SAS exome

AF:

0.686

Gnomad FIN exome

AF:

0.500

Gnomad NFE exome

AF:

0.568

Gnomad OTH exome

AF:

0.583

GnomAD4 exome

AF:

0.580

AC:

794678

AN:

1371068

Hom.:

235921

Cov.:

AF XY:

0.583

AC XY:

399242

AN XY:

685176

show subpopulations

Gnomad4 AFR exome

AF:

0.229

Gnomad4 AMR exome

AF:

0.647

Gnomad4 ASJ exome

AF:

0.512

Gnomad4 EAS exome

AF:

0.925

Gnomad4 SAS exome

AF:

0.682

Gnomad4 FIN exome

AF:

0.501

Gnomad4 NFE exome

AF:

0.573

Gnomad4 OTH exome

AF:

0.572

GnomAD4 genome

AF:

0.497

AC:

75436

AN:

151752

Hom.:

20957

Cov.:

AF XY:

0.502

AC XY:

37238

AN XY:

74184

show subpopulations

Gnomad4 AFR

AF:

0.246

Gnomad4 AMR

AF:

0.624

Gnomad4 ASJ

AF:

0.520

Gnomad4 EAS

AF:

0.909

Gnomad4 SAS

AF:

0.704

Gnomad4 FIN

AF:

0.492

Gnomad4 NFE

AF:

0.572

Gnomad4 OTH

AF:

0.546

Alfa

AF:

0.444

Hom.:

2347

Bravo

AF:

0.496

Asia WGS

AF:

0.768

AC:

2662

AN:

3470

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 14, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

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

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.16

DANN

Benign

0.64

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