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  • No ClinVar Id was directly found from the curated document


Variant: NM_175914.5:c.427-2A>G

CA409105868

Gene: HNF4A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: d54666ed-6c16-4627-866b-06dd61166fee
Approved on: 2023-05-27
Published on: 2023-05-27

HGVS expressions

NM_175914.5:c.427-2A>G
NC_000020.11:g.44414505A>G
CM000682.2:g.44414505A>G
NC_000020.10:g.43043145A>G
CM000682.1:g.43043145A>G
NC_000020.9:g.42476559A>G
NG_009818.1:g.63705A>G
ENST00000316099.10:c.493-2A>G
ENST00000619550.5:n.467-2A>G
ENST00000683148.1:n.469-2A>G
ENST00000683657.1:n.1617-2A>G
ENST00000316099.9:c.493-2A>G
ENST00000316099.8:c.493-2A>G
ENST00000316673.8:c.427-2A>G
ENST00000372920.1:c.*260-2A>G
ENST00000415691.2:c.493-2A>G
ENST00000443598.6:c.493-2A>G
ENST00000457232.5:c.427-2A>G
ENST00000609795.5:c.427-2A>G
ENST00000619550.4:c.418-2A>G
NM_000457.4:c.493-2A>G
NM_001030003.2:c.427-2A>G
NM_001030004.2:c.427-2A>G
NM_001258355.1:c.472-2A>G
NM_001287182.1:c.418-2A>G
NM_001287183.1:c.418-2A>G
NM_001287184.1:c.418-2A>G
NM_175914.4:c.427-2A>G
NM_178849.2:c.493-2A>G
NM_178850.2:c.493-2A>G
NM_001030003.3:c.427-2A>G
NM_001030004.3:c.427-2A>G
NM_001258355.2:c.472-2A>G
NM_001287182.2:c.418-2A>G
NM_001287184.2:c.418-2A>G
NM_178849.3:c.493-2A>G
NM_178850.3:c.493-2A>G
NM_000457.5:c.493-2A>G
NM_000457.6:c.493-2A>G
NM_001287183.2:c.418-2A>G
More

Likely Pathogenic

Met criteria codes 4
PM2_Supporting PP4_Moderate PVS1_Strong PP1
Not Met criteria codes 1
PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Monogenic Diabetes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for HNF4A Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.427-2A>G variant in the HNF4A gene, is predicted to remove a canonical splice acceptor site in intron 4 of NM_175914.4. This variant is predicted to cause an in-frame deletion of biologically-relevant exon 5 of 10, removing more than 10% of the protein (PVS1_Strong). This variant was identified in three unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal laboratory collaborators, PMID 36504295). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant segregated with diabetes, with three informative meioses in 1 family with MODY (PP1; internal laboratory collaborators). This variant was identified in at least 2 individuals with a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and history of macrosomia and neonatal hypoglycemia) (PP4_Moderate; internal laboratory collaborators). In summary, c.427-2A>G meets the criteria to be classified as likely pathogenic for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.0.0, approved 11/16/2022): PVS1_Strong, PM2_Supporting, PP1, PP4_Moderate.
Met criteria codes
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PP4_Moderate
This variant was identified in at least 2 individuals with a clinical history highly specific for HNF4A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF1A, and history of macrosomia and neonatal hypoglycemia) (PP4_Moderate; internal laboratory collaborators).
PVS1_Strong
The c.427-2A>G variant in the HNF4A gene, is predicted to remove a canonical splice acceptor site in intron 4 of NM_175914.4. This variant is predicted to cause an in-frame deletion of biologically-relevant exon 5 of 10, removing more than 10% of the protein (PVS1_Strong).
PP1
This variant segregated with diabetes, with three informative meioses in 1 family with MODY (PP1; internal laboratory collaborators).
Not Met criteria codes
PS4
This variant was identified in three unrelated individuals with non-autoimmune and non-absolute/near-absolute insulin-deficient diabetes; however, PS4_Moderate cannot be applied because this number is below the ClinGen MDEP threshold (internal laboratory collaborators, PMID 36504295).
Curation History
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