rs11164634

Variant names:

Your query was ambiguous. Multiple possible variants found:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001854.4(COL11A1):c.4303-47T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 1,516,076 control chromosomes in the GnomAD database, including 11,926 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1339 hom., cov: 32)

Exomes 𝑓: 0.11 ( 10587 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.12

Publications

6 publications found

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 Gene-Disease associations (from GenCC):

Marshall syndrome
Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp
Stickler syndrome type 2
Inheritance: AD, AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, PanelApp Australia, Orphanet, Genomics England PanelApp
fibrochondrogenesis 1
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
hearing loss, autosomal dominant 37
Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
autosomal dominant myopia-midfacial retrusion-sensorineural hearing loss-rhizomelic dysplasia syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
fibrochondrogenesis
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
autosomal recessive Stickler syndrome
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

COL11A1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 1-102890551-A-G is Benign according to our data. Variant chr1-102890551-A-G is described in ClinVar as Benign. ClinVar VariationId is 258465.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001854.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
COL11A1	NM_001854.4	MANE Select	c.4303-47T>C	intron	N/A	NP_001845.3
COL11A1	NM_080629.3		c.4339-47T>C	intron	N/A	NP_542196.2
COL11A1	NM_001190709.2		c.4186-47T>C	intron	N/A	NP_001177638.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
COL11A1	ENST00000370096.9	TSL:1 MANE Select	c.4303-47T>C	intron	N/A	ENSP00000359114.3
COL11A1	ENST00000512756.5	TSL:1	c.3955-47T>C	intron	N/A	ENSP00000426533.1
COL11A1	ENST00000635193.1	TSL:1	n.*1553-47T>C	intron	N/A	ENSP00000489428.1

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18565

AN:

151782

Hom.:

1341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.0307

Gnomad AMR

AF:

0.0900

Gnomad ASJ

AF:

0.0683

Gnomad EAS

AF:

0.249

Gnomad SAS

AF:

0.232

Gnomad FIN

AF:

0.0421

Gnomad MID

AF:

0.0601

Gnomad NFE

AF:

0.103

Gnomad OTH

AF:

0.115

GnomAD2 exomes

AF:

0.127

AC:

24249

AN:

191316

AF XY:

0.128

show subpopulations

Gnomad AFR exome

AF:

0.169

Gnomad AMR exome

AF:

0.101

Gnomad ASJ exome

AF:

0.0701

Gnomad EAS exome

AF:

0.277

Gnomad FIN exome

AF:

0.0481

Gnomad NFE exome

AF:

0.103

Gnomad OTH exome

AF:

0.105

GnomAD4 exome

AF:

0.115

AC:

156680

AN:

1364182

Hom.:

10587

Cov.:

AF XY:

0.117

AC XY:

79251

AN XY:

679526

show subpopulations

African (AFR)

AF:

0.169

AC:

4978

AN:

29506

American (AMR)

AF:

0.0957

AC:

3296

AN:

34438

Ashkenazi Jewish (ASJ)

AF:

0.0674

AC:

1628

AN:

24162

East Asian (EAS)

AF:

0.295

AC:

11407

AN:

38630

South Asian (SAS)

AF:

0.208

AC:

15921

AN:

76634

European-Finnish (FIN)

AF:

0.0510

AC:

2611

AN:

51244

Middle Eastern (MID)

AF:

0.0950

AC:

521

AN:

5486

European-Non Finnish (NFE)

AF:

0.105

AC:

109856

AN:

1047748

Other (OTH)

AF:

0.115

AC:

6462

AN:

56334

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

6441

12882

19324

25765

32206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

4246

8492

12738

16984

21230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.122

AC:

18568

AN:

151894

Hom.:

1339

Cov.:

AF XY:

0.120

AC XY:

8926

AN XY:

74234

show subpopulations

African (AFR)

AF:

0.166

AC:

6869

AN:

41490

American (AMR)

AF:

0.0900

AC:

1370

AN:

15228

Ashkenazi Jewish (ASJ)

AF:

0.0683

AC:

237

AN:

3468

East Asian (EAS)

AF:

0.249

AC:

1288

AN:

5180

South Asian (SAS)

AF:

0.230

AC:

1110

AN:

4816

European-Finnish (FIN)

AF:

0.0421

AC:

442

AN:

10498

Middle Eastern (MID)

AF:

0.0578

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.103

AC:

6969

AN:

67904

Other (OTH)

AF:

0.113

AC:

238

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

814

1628

2441

3255

4069

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0729

Hom.:

164

Bravo

AF:

0.125

Asia WGS

AF:

0.227

AC:

787

AN:

3468

ClinVar

ClinVar submissions as Germline

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.50

(source)

DANN

Benign

0.27

PhyloP100

-1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

ClinVar submissions as Germline

Computational scores

Splicing

Publications

Other links and lift over