Evidence Repository - Clinical Genome Resources

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

Link to SEPIO compliant JSON-LD document

Variant: NM_000545.8(HNF1A):c.1623+3A>G

CA10587145

256598 (ClinVar)

Gene: HNF1A

Condition: monogenic diabetes

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 4d08e15d-7c27-4174-9937-728646b86912

Approved on: 2022-05-03

Published on: 2022-05-03

HGVS expressions

NM_000545.8:c.1623+3A>G

NM_000545.8(HNF1A):c.1623+3A>G

NC_000012.12:g.120999392A>G

CM000674.2:g.120999392A>G

NC_000012.11:g.121437195A>G

CM000674.1:g.121437195A>G

NC_000012.10:g.119921578A>G

NG_011731.2:g.25647A>G

ENST00000257555.11:c.1623+3A>G

ENST00000257555.10:c.1623+3A>G

ENST00000540108.1:c.*1063+3A>G

ENST00000541395.5:c.1626A>G

ENST00000543427.5:c.1086+3A>G

ENST00000544413.2:c.1623+3A>G

ENST00000560968.5:n.1440+3A>G

ENST00000615446.4:c.411+3A>G

ENST00000617366.4:c.*32+3A>G

NM_000545.5:c.1623+3A>G

NM_000545.6:c.1623+3A>G

NM_001306179.1:c.1623+3A>G

NM_001306179.2:c.1623+3A>G

Uncertain Significance

BP4 PM2_Supporting

Evidence Links 0

Expert Panel

Monogenic Diabetes VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Monogenic Diabetes VCEP

The c.1623+3A>G variant in the HNF1 homeobox A gene, HNF1A, is predicted to remove a canonical splice donor site in intron 8 of NM_000545.8. This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computational splicing predictor SpliceAI gives a score of 0.0 for donor loss, suggesting that the variant has no impact on splicing (BP4). In summary, c.1623+3A>G 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, BP4.

BP4

The computational splicing predictor SpliceAI gives a score of 0.00 for donor/acceptor loss, suggesting that the variant has no impact on splicing.

PM2_Supporting

Absent from gnomAD.

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