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Variant: NM_000545.6(HNF1A):c.1548C>T (p.Gly516=)

CA10587144

256597 (ClinVar)

Gene: HNF1A
Condition: monogenic diabetes
Inheritance Mode: Autosomal dominant inheritance
UUID: 09564224-5807-4d6b-b8dc-ce4a211ca180
Approved on: 2022-05-02
Published on: 2022-05-02

HGVS expressions

NM_000545.6:c.1548C>T
NM_000545.6(HNF1A):c.1548C>T (p.Gly516=)
NC_000012.12:g.120999314C>T
CM000674.2:g.120999314C>T
NC_000012.11:g.121437117C>T
CM000674.1:g.121437117C>T
NC_000012.10:g.119921500C>T
NG_011731.2:g.25569C>T
ENST00000257555.11:c.1548C>T
ENST00000257555.10:c.1548C>T
ENST00000540108.1:c.*988C>T
ENST00000541395.5:c.1548C>T
ENST00000543427.5:c.1011C>T
ENST00000544413.2:c.1548C>T
ENST00000560968.5:n.1365C>T
ENST00000615446.4:c.336C>T
ENST00000617366.4:c.665C>T
NM_000545.5:c.1548C>T
NM_001306179.1:c.1548C>T
NM_000545.8:c.1548C>T
NM_001306179.2:c.1548C>T
NM_000545.8(HNF1A):c.1548C>T (p.Gly516=)
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Uncertain Significance

Met criteria codes 1
PM2_Supporting
Not Met criteria codes 2
PP3 BP7

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Monogenic Diabetes VCEP
The c.1548C>T variant in the HNF1 homeobox A gene, HNF1A, is a synonymous (silent) variant at codon 516 (p.(Gly516=)) of NM_000545.8. This variant has a minor allele frequency of 0.0000088 in the gnomAD v2.1.1 European non-Finnish population and no copies in another subpopulation, which is less than the ClinGen MDEP threshold for PM2_Supporting (≤0.00002 and ≤1 copy in any other subpopulation) (PM2_Supporting). BP7 was not applied for this synonymous variant because SpliceAI predicts an impact on splicing, specifically a gain of a novel splice acceptor site (score = 0.47); however, PP3 was not applied because an acceptor loss was not predicted (score = 0.03). In summary, c.1548C>T 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.
Met criteria codes
PM2_Supporting
This variant has a minor allele frequency in gnomAD of less than 0.00002 in the European non-Finnish population (actual value = 0.0000088) and zero copies in any other population.
Not Met criteria codes
PP3
An acceptor gain (score = 0.47) but not an acceptor loss (score = 0.03) is predicted by Splice AI.
BP7
BP7 was not applied for this synonymous variant because SpliceAI predicts an acceptor gain with a score of 0.47. Acceptor loss is not predicted, however.
Curation History
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