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

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Variant: NM_000545.6(HNF1A):c.526+2dup

CA658658176

447494 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 02476433-cb6b-488a-8d31-1acbb44e90ce

HGVS expressions

NM_000545.6:c.526+2dup
NM_000545.6(HNF1A):c.526+2dup
NC_000012.12:g.120989034dup
CM000674.2:g.120989034dup
NC_000012.11:g.121426837dup
CM000674.1:g.121426837dup
NC_000012.10:g.119911220dup
NG_011731.2:g.15289dup
ENST00000257555.11:c.526+2dup
ENST00000257555.10:c.526+2dup
ENST00000400024.6:c.526+2dup
ENST00000402929.5:n.661+2dup
ENST00000535955.5:n.43-8457dup
ENST00000538626.2:n.191-8457dup
ENST00000538646.5:c.526+2dup
ENST00000540108.1:c.327-4486dup
ENST00000541395.5:c.526+2dup
ENST00000541924.5:c.526+2dup
ENST00000543427.5:c.526+2dup
ENST00000544413.2:c.526+2dup
ENST00000544574.5:c.73-7583dup
ENST00000560968.5:n.669+2dup
ENST00000615446.4:c.-257-7228dup
ENST00000617366.4:c.526+2dup
NM_000545.5:c.526+2dup
NM_001306179.1:c.526+2dup
NM_000545.8:c.526+2dup
NM_001306179.2:c.526+2dup
NM_000545.8(HNF1A):c.526+2dup

Uncertain Significance

Met criteria codes 3
PP4_Moderate PP3 PM2_Supporting
Not Met criteria codes 1
PS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.526+2dup variant in the HNF1 homeobox A gene, HNF1A, is predicted to remove a canonical splice donor site in intron 2 of NM_000545.8. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was also identified in an individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and response to low dose sulfonylureas) (PP4_Moderate; internal lab contributors). The computational splicing predictor SpliceAI gives a score of 0.48 for donor loss, predicting that the variant disrupts the donor site of intron 2 of HNF1A (PP3). 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 lab contributors). In summary, c.526+2dup meets the criteria to be classified as a variant of uncertain significance for monogenic diabetes. ACMG/AMP criteria applied, as specified by the ClinGen MDEP (specification version 1.1, approved 9/30/2021): PM2_Supporting, PP4_Moderate, PP3.
Met criteria codes
PP4_Moderate
This variant was identified in one individual with a clinical history highly specific for HNF1A-MODY (MODY probability calculator result >50%, negative genetic testing for HNF4A, and sulfonylurea-responsive) (internal lab contributor).
PP3
The computational splicing predictor SpliceAI gives a score of 0.48 for donor loss, predicting that the variant disrupts the donor site of intron 2 of HNF1A.
PM2_Supporting
This variant is absent from gnomAD.
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 lab contributors).
Approved on: 2022-04-15
Published on: 2022-04-15
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