Variant 1-102890551-A-G 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.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

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=-0.85).

BP6

Variant 1-102890551-A-G is Benign according to our data. Variant chr1-102890551-A-G is described in ClinVar as [Benign]. Clinvar id 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL11A1	NM_001854.4 linkuse as main transcript	c.4303-47T>C		intron_variant		ENST00000370096.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL11A1	ENST00000370096.9 linkuse as main transcript	c.4303-47T>C		intron_variant		1	NM_001854.4	P1	P12107-1

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

GnomAD3 exomes

AF:

0.127

AC:

24249

AN:

191316

Hom.:

1917

AF XY:

0.128

AC XY:

13260

AN XY:

103726

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 SAS exome

AF:

0.222

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

Gnomad4 AFR exome

AF:

0.169

Gnomad4 AMR exome

AF:

0.0957

Gnomad4 ASJ exome

AF:

0.0674

Gnomad4 EAS exome

AF:

0.295

Gnomad4 SAS exome

AF:

0.208

Gnomad4 FIN exome

AF:

0.0510

Gnomad4 NFE exome

AF:

0.105

Gnomad4 OTH exome

AF:

0.115

GnomAD4 genome

AF:

0.122

AC:

18568

AN:

151894

Hom.:

1339

Cov.:

AF XY:

0.120

AC XY:

8926

AN XY:

74234

show subpopulations

Gnomad4 AFR

AF:

0.166

Gnomad4 AMR

AF:

0.0900

Gnomad4 ASJ

AF:

0.0683

Gnomad4 EAS

AF:

0.249

Gnomad4 SAS

AF:

0.230

Gnomad4 FIN

AF:

0.0421

Gnomad4 NFE

AF:

0.103

Gnomad4 OTH

AF:

0.113

Alfa

AF:

0.0706

Hom.:

149

Bravo

AF:

0.125

Asia WGS

AF:

0.227

AC:

787

AN:

3468

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

-0.85

CADD

Benign

0.50

DANN

Benign

0.27

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