NM_175914.5(HNF4A):c.50-5C>T AND not specified

Germline classification:: Benign (3 submissions)
Last evaluated:: Apr 24, 2019
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:: RCV000117237.18

Allele description [Variation Report for NM_175914.5(HNF4A):c.50-5C>T]

NM_175914.5(HNF4A):c.50-5C>T

Gene:

HNF4A:hepatocyte nuclear factor 4 alpha [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.12

Genomic location:

Preferred name:

NM_175914.5(HNF4A):c.50-5C>T

HGVS:

NC_000020.11:g.44406053C>T
NG_009818.1:g.55253C>T
NM_000457.6:c.116-5C>T
NM_001030003.3:c.50-5C>T
NM_001030004.3:c.50-5C>T
NM_001258355.2:c.95-5C>T
NM_001287182.2:c.41-5C>T
NM_001287183.2:c.41-5C>T
NM_001287184.2:c.41-5C>T
NM_175914.5:c.50-5C>TMANE SELECT
NM_178849.3:c.116-5C>T
NM_178850.3:c.116-5C>T
LRG_483t1:c.50-5C>T
LRG_483t2:c.116-5C>T
LRG_483:g.55253C>T
NC_000020.10:g.43034693C>T
NM_000457.4:c.116-5C>T
NM_175914.3:c.50-5C>T
NM_175914.4:c.50-5C>T

Links:

dbSNP: rs745975

NCBI 1000 Genomes Browser:

rs745975

Molecular consequence:

NM_000457.6:c.116-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001030003.3:c.50-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001030004.3:c.50-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001258355.2:c.95-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001287182.2:c.41-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001287183.2:c.41-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_001287184.2:c.41-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_175914.5:c.50-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_178849.3:c.116-5C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_178850.3:c.116-5C>T - intron variant - [Sequence Ontology: SO:0001627]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000151410	Genetic Services Laboratory, University of Chicago	no assertion criteria provided	Likely benign	germline	clinical testing
SCV000316595	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001365799	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Apr 24, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000151410

Genetic Services Laboratory, University of Chicago

no assertion criteria provided

Likely benign

germline

clinical testing

SCV000316595

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001365799

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Apr 24, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Genetic Services Laboratory, University of Chicago, SCV000151410.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From PreventionGenetics, part of Exact Sciences, SCV000316595.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV001365799.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

The c.95-5C>T variant in HNF4A is classified as benign because it has been identified in 19.56% (55114/281792) of total chromosomes by gnomAD (http://gnomad.broadinstitute.org/). Additionally, this variant does not alter the splice consensus sequence and is not predicted to impact splicing. ACMG/AMP criteria applied: BA1, BP4.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		1	not provided	1	not provided

Last Updated: May 1, 2024

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