Variant rs3767272 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.1413+47A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.028 in 1,453,522 control chromosomes in the GnomAD database, including 734 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 61 hom., cov: 32)

Exomes 𝑓: 0.028 ( 673 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.0650

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=-0.89).

BP6

Variant 1-103017773-T-C is Benign according to our data. Variant chr1-103017773-T-C is described in ClinVar as [Benign]. Clinvar id is 674969.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0611 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.1413+47A>G		intron_variant		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.1413+47A>G		intron_variant		1	NM_001854.4	ENSP00000359114	P1	P12107-1

Frequencies

GnomAD3 genomes

AF:

0.0241

AC:

3671

AN:

152100

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0142

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0274

Gnomad ASJ

AF:

0.0421

Gnomad EAS

AF:

0.0668

Gnomad SAS

AF:

0.0534

Gnomad FIN

AF:

0.00273

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.0263

Gnomad OTH

AF:

0.0291

GnomAD3 exomes

AF:

0.0299

AC:

7509

AN:

250830

Hom.:

170

AF XY:

0.0321

AC XY:

4349

AN XY:

135574

show subpopulations

Gnomad AFR exome

AF:

0.0128

Gnomad AMR exome

AF:

0.0159

Gnomad ASJ exome

AF:

0.0435

Gnomad EAS exome

AF:

0.0750

Gnomad SAS exome

AF:

0.0484

Gnomad FIN exome

AF:

0.00315

Gnomad NFE exome

AF:

0.0284

Gnomad OTH exome

AF:

0.0285

GnomAD4 exome

AF:

0.0284

AC:

36981

AN:

1301304

Hom.:

673

Cov.:

AF XY:

0.0293

AC XY:

19242

AN XY:

656534

show subpopulations

Gnomad4 AFR exome

AF:

0.0140

Gnomad4 AMR exome

AF:

0.0166

Gnomad4 ASJ exome

AF:

0.0429

Gnomad4 EAS exome

AF:

0.0606

Gnomad4 SAS exome

AF:

0.0484

Gnomad4 FIN exome

AF:

0.00422

Gnomad4 NFE exome

AF:

0.0272

Gnomad4 OTH exome

AF:

0.0297

GnomAD4 genome

AF:

0.0242

AC:

3683

AN:

152218

Hom.:

Cov.:

AF XY:

0.0241

AC XY:

1790

AN XY:

74406

show subpopulations

Gnomad4 AFR

AF:

0.0145

Gnomad4 AMR

AF:

0.0274

Gnomad4 ASJ

AF:

0.0421

Gnomad4 EAS

AF:

0.0669

Gnomad4 SAS

AF:

0.0536

Gnomad4 FIN

AF:

0.00273

Gnomad4 NFE

AF:

0.0263

Gnomad4 OTH

AF:

0.0293

Alfa

AF:

0.0259

Hom.:

Bravo

AF:

0.0252

Asia WGS

AF:

0.0440

AC:

151

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 14, 2018	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, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.6

DANN

Benign

0.32

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