12-120978485-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000433033.3(HNF1A-AS1):n.134+1129G>A variant causes a intron change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★★).
Frequency
Consequence
ENST00000433033.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
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Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNF1A-AS1 | ENST00000433033.3 | n.134+1129G>A | intron_variant | Intron 1 of 3 | 3 | |||||
HNF1A-AS1 | ENST00000535301.2 | n.322+2159G>A | intron_variant | Intron 1 of 1 | 4 | |||||
HNF1A-AS1 | ENST00000537361.1 | n.263+2159G>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 359756Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 189662
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Monogenic diabetes Uncertain:1
The c.-284C>T variant in the HNF1 homeobox A gene, HNF1A, is a single nucleotide variant in the promoter region of NM_000545.8. This variant is located within the HNF4A binding site (–c.-276 to c.-288) of the promoter HNF1A, which is defined as critical for the protein’s function by the ClinGen MDEP (PM1_Supporting). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). This variant was identified in an individual with a clinical history highly specific for HNF1A-monogenic diabetes (MODY probability calculator result >50%, negative genetic testing for HNF4A, negative antibodies, and >=3 generation family history of diabetes) (PP4_Moderate; internal lab contributors). In summary, c.-284C>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 2.1.0, approved 8/11/2023): PP4_Moderate, PM1_Supporting, PM2_Supporting. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.