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NM_001854.4(COL11A1):c.2916+3A>G AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Nov 7, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000658519.22

Allele description [Variation Report for NM_001854.4(COL11A1):c.2916+3A>G]

NM_001854.4(COL11A1):c.2916+3A>G

Gene:
COL11A1:collagen type XI alpha 1 chain [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p21.1
Genomic location:
Preferred name:
NM_001854.4(COL11A1):c.2916+3A>G
HGVS:
  • NC_000001.11:g.102965484T>C
  • NG_008033.2:g.148013A>G
  • NM_001190709.2:c.2799+3A>G
  • NM_001854.4:c.2916+3A>GMANE SELECT
  • NM_080629.3:c.2952+3A>G
  • NM_080630.4:c.2568+3A>G
  • NC_000001.10:g.103431040T>C
  • NC_000001.10:g.103431040T>C
  • NM_001854.3:c.2916+3A>G
Links:
dbSNP: rs200515572
NCBI 1000 Genomes Browser:
rs200515572
Molecular consequence:
  • NM_001190709.2:c.2799+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001854.4:c.2916+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_080629.3:c.2952+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_080630.4:c.2568+3A>G - intron variant - [Sequence Ontology: SO:0001627]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000780291CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)
Uncertain significance
(Mar 1, 2018)
germlineclinical testing

Citation Link,

SCV003023944Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Nov 7, 2023)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (3)

Details of each submission

From CeGaT Center for Human Genetics Tuebingen, SCV000780291.26

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

From Invitae, SCV003023944.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change falls in intron 38 of the COL11A1 gene. It does not directly change the encoded amino acid sequence of the COL11A1 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs200515572, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with COL11A1-related conditions. ClinVar contains an entry for this variant (Variation ID: 507173). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jul 23, 2024