12-120978369-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The ENST00000433033.3(HNF1A-AS1):n.134+1245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00183 in 152,312 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000433033.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 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+1245G>A | intron_variant | Intron 1 of 3 | 3 | |||||
HNF1A-AS1 | ENST00000535301.2 | n.322+2275G>A | intron_variant | Intron 1 of 1 | 4 | |||||
HNF1A-AS1 | ENST00000537361.1 | n.263+2275G>A | intron_variant | Intron 1 of 1 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00185 AC: 282AN: 152194Hom.: 0 Cov.: 31
GnomAD4 genome AF: 0.00183 AC: 279AN: 152312Hom.: 0 Cov.: 31 AF XY: 0.00187 AC XY: 139AN XY: 74478
ClinVar
Submissions by phenotype
Maturity onset diabetes mellitus in young Benign:1
Mutations in HNF1A gene can predispose to MODY3. It is associated with both micro and macrovascular complications of diabetes, especially cardiovascular complications. Associated with glucosuria. May respond well to sulfonylureas. However, more evidence is required to confer the association of this particular variant rs77774709 with MODY3. -
not provided Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at