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NM_001854.4(COL11A1):c.3492+3G>A AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Oct 13, 2023
Review status:
criteria provided, conflicting classifications
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:
RCV001905228.9

Allele description [Variation Report for NM_001854.4(COL11A1):c.3492+3G>A]

NM_001854.4(COL11A1):c.3492+3G>A

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.3492+3G>A
HGVS:
  • NC_000001.11:g.102935057C>T
  • NG_008033.2:g.178440G>A
  • NM_001190709.2:c.3375+3G>A
  • NM_001854.3:c.3492+3G>A
  • NM_001854.4:c.3492+3G>AMANE SELECT
  • NM_080629.3:c.3528+3G>A
  • NM_080630.4:c.3144+3G>A
  • NC_000001.10:g.103400613C>T
Links:
dbSNP: rs372941709
NCBI 1000 Genomes Browser:
rs372941709
Molecular consequence:
  • NM_001190709.2:c.3375+3G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001854.4:c.3492+3G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_080629.3:c.3528+3G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_080630.4:c.3144+3G>A - intron variant - [Sequence Ontology: SO:0001627]

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
SCV002132046Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Oct 13, 2023)
germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

SCV002504222GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)
Likely benign
(Apr 7, 2020)
germlineclinical testing

Citation Link

Summary from all submissions

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

Citations

PubMed

Collagen XI sequence variations in nonsyndromic cleft palate, Robin sequence and micrognathia.

Melkoniemi M, Koillinen H, Männikkö M, Warman ML, Pihlajamaa T, Kääriäinen H, Rautio J, Hukki J, Stofko JA, Cisneros GJ, Krakow D, Cohn DH, Kere J, Ala-Kokko L.

Eur J Hum Genet. 2003 Mar;11(3):265-70.

PubMed [citation]
PMID:
12673280

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
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV002132046.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change falls in intron 45 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 (rs372941709, gnomAD 0.2%). This variant has been observed in individual(s) with clinical features of COL11A1-related conditions ‚Äã (PMID: 12673280). This variant is also known as IVS45+3G>A. ClinVar contains an entry for this variant (Variation ID: 1364086). 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 is not likely to affect RNA splicing. 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

From GeneDx, SCV002504222.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

See Variant Classification Assertion Criteria.

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

Last Updated: Jul 7, 2024