dbSNP rs17127203: COL11A1:c.4608+18A>G (chr1-102888559-T-C) – 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.4608+18A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 1,607,942 control chromosomes in the GnomAD database, including 13,632 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.12 ( 1360 hom., cov: 33)

Exomes 𝑓: 0.12 ( 12272 hom. )

Consequence

COL11A1
NM_001854.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -0.0560

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=-0.82).

BP6

Variant 1-102888559-T-C is Benign according to our data. Variant chr1-102888559-T-C is described in ClinVar as [Benign]. Clinvar id is 258467.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-102888559-T-C is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.235 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COL11A1	NM_001854.4 link	c.4608+18A>G		intron_variant	Intron 62 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.4608+18A>G		intron_variant	Intron 62 of 66	1	NM_001854.4	ENSP00000359114.3		P12107-1

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

19015

AN:

152108

Hom.:

1362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.163

Gnomad AMI

AF:

0.0340

Gnomad AMR

AF:

0.0929

Gnomad ASJ

AF:

0.0732

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.242

Gnomad FIN

AF:

0.0437

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.117

GnomAD3 exomes

AF:

0.131

AC:

32699

AN:

250224

Hom.:

2671

AF XY:

0.133

AC XY:

18030

AN XY:

135350

show subpopulations

Gnomad AFR exome

AF:

0.163

Gnomad AMR exome

AF:

0.102

Gnomad ASJ exome

AF:

0.0752

Gnomad EAS exome

AF:

0.271

Gnomad SAS exome

AF:

0.228

Gnomad FIN exome

AF:

0.0479

Gnomad NFE exome

AF:

0.108

Gnomad OTH exome

AF:

0.110

GnomAD4 exome

AF:

0.120

AC:

175342

AN:

1455716

Hom.:

12272

Cov.:

AF XY:

0.123

AC XY:

88972

AN XY:

724614

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.0999

Gnomad4 ASJ exome

AF:

0.0748

Gnomad4 EAS exome

AF:

0.295

Gnomad4 SAS exome

AF:

0.220

Gnomad4 FIN exome

AF:

0.0516

Gnomad4 NFE exome

AF:

0.110

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.125

AC:

19016

AN:

152226

Hom.:

1360

Cov.:

AF XY:

0.123

AC XY:

9182

AN XY:

74418

show subpopulations

Gnomad4 AFR

AF:

0.163

Gnomad4 AMR

AF:

0.0929

Gnomad4 ASJ

AF:

0.0732

Gnomad4 EAS

AF:

0.246

Gnomad4 SAS

AF:

0.241

Gnomad4 FIN

AF:

0.0437

Gnomad4 NFE

AF:

0.108

Gnomad4 OTH

AF:

0.115

Alfa

AF:

0.116

Hom.:

245

Bravo

AF:

0.127

Asia WGS

AF:

0.230

AC:

800

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:4

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Oct 03, 2016

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. -

Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

5.5

DANN

Benign

0.42

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