rs113495257
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_175914.5(HNF4A):c.583-27G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000695 in 1,600,480 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). There are indicators that this mutation may affect the branch point..
Frequency
Consequence
NM_175914.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HNF4A | NM_175914.5 | c.583-27G>A | intron_variant | ENST00000316673.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HNF4A | ENST00000316673.9 | c.583-27G>A | intron_variant | 1 | NM_175914.5 |
Frequencies
GnomAD3 genomes ? AF: 0.00371 AC: 564AN: 152210Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000917 AC: 230AN: 250926Hom.: 3 AF XY: 0.000781 AC XY: 106AN XY: 135654
GnomAD4 exome AF: 0.000378 AC: 548AN: 1448152Hom.: 2 Cov.: 29 AF XY: 0.000324 AC XY: 234AN XY: 721318
GnomAD4 genome ? AF: 0.00370 AC: 564AN: 152328Hom.: 1 Cov.: 31 AF XY: 0.00356 AC XY: 265AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 03, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Maturity onset diabetes mellitus in young Benign:1
Benign, criteria provided, single submitter | research | Clinical Genomics, Uppaluri K&H Personalized Medicine Clinic | - | Potent mutations in HNF4A are associated with poor insulin secretion in response to hyperglycemia. Associated with MODY1. Patients initially respond well to sulfonylureas but eventually become insulin dependent. However, more evidence is required to ascertain the role of this particular variant rs113495257 in MODY, yet. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at