20-44355722-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_175914.5(HNF4A):c.-83C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000699 in 1,259,794 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 Uncertain risk allele (★★).
Frequency
Consequence
NM_175914.5 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HNF4A | NM_175914.5 | c.-83C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | ENST00000316673.9 | NP_787110.2 | ||
HNF4A | NM_175914.5 | c.-83C>T | 5_prime_UTR_variant | Exon 1 of 10 | ENST00000316673.9 | NP_787110.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNF4A | ENST00000316673 | c.-83C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 10 | 1 | NM_175914.5 | ENSP00000315180.4 | |||
HNF4A | ENST00000316673 | c.-83C>T | 5_prime_UTR_variant | Exon 1 of 10 | 1 | NM_175914.5 | ENSP00000315180.4 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152236Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000686 AC: 76AN: 1107558Hom.: 0 Cov.: 15 AF XY: 0.0000688 AC XY: 39AN XY: 566918
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
- -
Maturity onset diabetes mellitus in young Other:1
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 rs879092890 in MODY, yet. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at