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NM_033380.3(COL4A5):c.-25_-8dup AND not provided

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Sep 1, 2022
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:
RCV000520002.10

Allele description [Variation Report for NM_033380.3(COL4A5):c.-25_-8dup]

NM_033380.3(COL4A5):c.-25_-8dup

Gene:
COL4A5:collagen type IV alpha 5 chain [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
Xq22.3
Genomic location:
Preferred name:
NM_033380.3(COL4A5):c.-25_-8dup
HGVS:
  • NC_000023.11:g.108440101_108440118dup
  • NG_011977.2:g.5178_5195dup
  • NG_012059.2:g.4358_4375dup
  • NM_000495.5:c.-25_-8dup
  • NM_033380.3:c.-25_-8dupMANE SELECT
  • LRG_232t1:c.-25_-8dup
  • LRG_232t2:c.-25_-8dup
  • LRG_232:g.5178_5195dup
  • LRG_233:g.4358_4375dup
  • NC_000023.10:g.107683331_107683348dup
  • NG_011977.1:g.5178_5195dup
  • NM_000495.4:c.-25_-8dup18
  • NM_000495.5:c.-25_-8dup18
  • NM_000495.5:c.-25_-8dupAAGGAGCTGCGGGAGCCG
  • NM_033380.1:c.-25_-8dupAAGGAGCTGCGGGAGCCG
Links:
dbSNP: rs752443408
NCBI 1000 Genomes Browser:
rs752443408
Molecular consequence:
  • NM_000495.5:c.-25_-8dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_033380.3:c.-25_-8dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000619826GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Aug 1, 2017) 		germlineclinical testing

Citation Link,

SCV004167393CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Likely benign
(Sep 1, 2022) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000619826.2

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

Description

This individual is also heterozygous for the c.-25_-8dup18 variant. It has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This regulatory duplication affects both nonconserved nucleotides and nucleotides conserved through mammals. No regulatory variants have been reported in the Human Gene Mutation Database or observed at GeneDx (Stenson et al., 2014). Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

From CeGaT Center for Human Genetics Tuebingen, SCV004167393.8

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

COL4A5: BS2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Aug 4, 2024