Variant rs6668897 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.488+23G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,598,358 control chromosomes in the GnomAD database, including 19,569 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.14 ( 1596 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17973 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0880

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=-0.77).

BP6

Variant 1-103078635-C-T is Benign according to our data. Variant chr1-103078635-C-T is described in ClinVar as [Benign]. Clinvar id is 258471.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.157 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.488+23G>A		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.488+23G>A		intron_variant		1	NM_001854.4	ENSP00000359114	P1	P12107-1

Frequencies

GnomAD3 genomes

AF:

0.138

AC:

20913

AN:

151816

Hom.:

1594

Cov.:

show subpopulations

Gnomad AFR

AF:

0.102

Gnomad AMI

AF:

0.0769

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.139

Gnomad EAS

AF:

0.00890

Gnomad SAS

AF:

0.0908

Gnomad FIN

AF:

0.207

Gnomad MID

AF:

0.143

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.127

GnomAD3 exomes

AF:

0.149

AC:

37255

AN:

250088

Hom.:

3137

AF XY:

0.147

AC XY:

19842

AN XY:

135268

show subpopulations

Gnomad AFR exome

AF:

0.102

Gnomad AMR exome

AF:

0.215

Gnomad ASJ exome

AF:

0.143

Gnomad EAS exome

AF:

0.00631

Gnomad SAS exome

AF:

0.100

Gnomad FIN exome

AF:

0.208

Gnomad NFE exome

AF:

0.161

Gnomad OTH exome

AF:

0.159

GnomAD4 exome

AF:

0.153

AC:

221820

AN:

1446424

Hom.:

17973

Cov.:

AF XY:

0.152

AC XY:

109760

AN XY:

720688

show subpopulations

Gnomad4 AFR exome

AF:

0.106

Gnomad4 AMR exome

AF:

0.211

Gnomad4 ASJ exome

AF:

0.142

Gnomad4 EAS exome

AF:

0.00692

Gnomad4 SAS exome

AF:

0.102

Gnomad4 FIN exome

AF:

0.207

Gnomad4 NFE exome

AF:

0.159

Gnomad4 OTH exome

AF:

0.151

GnomAD4 genome

AF:

0.138

AC:

20936

AN:

151934

Hom.:

1596

Cov.:

AF XY:

0.138

AC XY:

10280

AN XY:

74256

show subpopulations

Gnomad4 AFR

AF:

0.102

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.139

Gnomad4 EAS

AF:

0.00892

Gnomad4 SAS

AF:

0.0909

Gnomad4 FIN

AF:

0.207

Gnomad4 NFE

AF:

0.159

Gnomad4 OTH

AF:

0.126

Alfa

AF:

0.157

Hom.:

496

Bravo

AF:

0.134

Asia WGS

AF:

0.0590

AC:

204

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

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 26, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

5.9

DANN

Benign

0.71

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