NM_000458.4(HNF1B):c.1045+12T>C AND Renal cysts and diabetes syndrome

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Jan 13, 2018)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000030519.3

Allele description [Variation Report for NM_000458.4(HNF1B):c.1045+12T>C]

NM_000458.4(HNF1B):c.1045+12T>C

Gene:
HNF1B:HNF1 homeobox B [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q12
Genomic location:
Preferred name:
NM_000458.4(HNF1B):c.1045+12T>C
HGVS:
  • NC_000017.11:g.37731583A>G
  • NG_013019.2:g.18524T>C
  • NM_000458.4:c.1045+12T>CMANE SELECT
  • NM_001165923.4:c.967+12T>C
  • NM_001304286.2:c.967+12T>C
  • NC_000017.10:g.36091574A>G
  • NM_000458.2:c.1045+12T>C
Links:
dbSNP: rs141166864
NCBI 1000 Genomes Browser:
rs141166864
Molecular consequence:
  • NM_000458.4:c.1045+12T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001165923.4:c.967+12T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001304286.2:c.967+12T>C - intron variant - [Sequence Ontology: SO:0001627]
Observations:
3

Condition(s)

Name:
Renal cysts and diabetes syndrome (RCAD)
Synonyms:
Maturity-onset diabetes of the young, type 5; MODY type 5; Hyperuricemic nephropathy, familial juvenile, atypical; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007669; MedGen: C0431693; Orphanet: 93111; OMIM: 137920

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000053190Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
uncertain
(Aug 18, 2011)
germlinecuration, clinical testing

Citation Link,

SCV000402431Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Benign
(Jan 13, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown3not providednot providednot providednot providedclinical testing
not providedgermlineyes1not providednot providednot providednot providedcuration

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000053190.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided
2not providednot providednot providednot providedclinical testingnot provided
3not providednot providednot providednot providedclinical testingnot provided
4not providednot providednot providednot providedclinical testingnot provided

Description

Converted during submission to Uncertain significance.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providedBloodassert pathogenicitynot providednot providednot providednot provided
2germlineunknownnot providedBloodassert pathogenicitynot providednot providednot provided See 2
3germlineunknownnot providedBloodassert pathogenicitynot providednot providednot provided See 3
4germlineunknownnot providedBloodassert pathogenicitynot providednot providednot provided See 4

Co-occurrences

#ZygosityAllelesNumber of Observations
2SingleHeterozygoteGCK:c.1253+8C>T, GCK:c.944T>C, TCF1:c.51C>G, TCF1:c.1545G>A, TCF1:c.1460G>A, TCF1:c.1375C>T, TCF1:c.864G>C, TCF1:c.1501+7G>A, TCF1:c.79A>C, TCF1:c.1720A>G1
3SingleHeterozygoteTCF1:c.1720A>G, TCF1:c.1545G>A, TCF1:c.864G>C1
4SingleHeterozygoteGCK:c.645C>T, GCK:c.1253+8C>T, IPF1:c.571A>C, TCF1:c.864G>C, TCF1:c.79A>C, TCF1:c.51C>G, TCF1:c.1720A>G1

From Illumina Clinical Services Laboratory,Illumina, SCV000402431.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

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

Last Updated: Jun 14, 2021

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