The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_175914.5(HNF4A):c.427-5C>T

CA209272

211146 (ClinVar)

Gene: HNF4A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 8b1721c7-708c-43a6-abe3-4931c8cee06a
Approved on: 2023-05-27
Published on: 2023-05-27

HGVS expressions

NM_175914.5:c.427-5C>T
NM_175914.5(HNF4A):c.427-5C>T
NC_000020.11:g.44414502C>T
CM000682.2:g.44414502C>T
NC_000020.10:g.43043142C>T
CM000682.1:g.43043142C>T
NC_000020.9:g.42476556C>T
NG_009818.1:g.63702C>T
ENST00000316099.10:c.493-5C>T
ENST00000619550.5:n.467-5C>T
ENST00000683148.1:n.469-5C>T
ENST00000683657.1:n.1617-5C>T
ENST00000316099.9:c.493-5C>T
ENST00000316099.8:c.493-5C>T
ENST00000316673.8:c.427-5C>T
ENST00000372920.1:c.*260-5C>T
ENST00000415691.2:c.493-5C>T
ENST00000443598.6:c.493-5C>T
ENST00000457232.5:c.427-5C>T
ENST00000609795.5:c.427-5C>T
ENST00000619550.4:c.418-5C>T
NM_000457.4:c.493-5C>T
NM_001030003.2:c.427-5C>T
NM_001030004.2:c.427-5C>T
NM_001258355.1:c.472-5C>T
NM_001287182.1:c.418-5C>T
NM_001287183.1:c.418-5C>T
NM_001287184.1:c.418-5C>T
NM_175914.4:c.427-5C>T
NM_178849.2:c.493-5C>T
NM_178850.2:c.493-5C>T
NM_001030003.3:c.427-5C>T
NM_001030004.3:c.427-5C>T
NM_001258355.2:c.472-5C>T
NM_001287182.2:c.418-5C>T
NM_001287184.2:c.418-5C>T
NM_178849.3:c.493-5C>T
NM_178850.3:c.493-5C>T
NM_000457.5:c.493-5C>T
NM_000457.6:c.493-5C>T
NM_001287183.2:c.418-5C>T
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Likely Benign

Met criteria codes 2
BP4 BS1

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.427-5C>T variant in the hepatocyte nuclear factor-4-alpha gene, HNF4A, is located in the non-canonical splice acceptor region five base pairs upstream of the intron 4/ exon 4 splice junction of NM_175914.5. This variant has a Popmax Filtering allele frequency in gnomAD 2.1.1 of 0.00006366, which is greater than the MDEP threshold for BS1 (0.000033) (BS1). The computational splicing predictor SpliceAI gives a score of 0.00 for acceptor loss/gain, suggesting that the variant has no impact on splicing. In summary, c.427-5C>T meets the criteria to be classified as likely benign for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDENmP (specification version 1.0.0, approved 11/16/2022): BP4, BS1.
Met criteria codes
BP4
The computational splicing predictor SpliceAI gives a score of 0.00 for acceptor loss/gain, suggesting that the variant has no impact on splicing.
BS1
This variant has a Popmax Filtering allele frequency in gnomAD 2.1.1 of 0.00006366, which is greater than the MDEP threshold for BS1 (0.000033) (BS1).
Curation History
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