20-44355787-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_175914.5(HNF4A):c.-18G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,612,884 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 significance (★★).
Frequency
Consequence
NM_175914.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNF4A | ENST00000316673 | c.-18G>A | 5_prime_UTR_variant | Exon 1 of 10 | 1 | NM_175914.5 | ENSP00000315180.4 | |||
HNF4A | ENST00000457232.5 | c.-18G>A | upstream_gene_variant | 1 | ENSP00000396216.1 | |||||
HNF4A | ENST00000609795.5 | c.-18G>A | upstream_gene_variant | 1 | ENSP00000476609.1 | |||||
HNF4A | ENST00000609262.5 | c.-249G>A | upstream_gene_variant | 1 | ENSP00000476310.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000366 AC: 9AN: 245724Hom.: 0 AF XY: 0.0000299 AC XY: 4AN XY: 133960
GnomAD4 exome AF: 0.0000199 AC: 29AN: 1460666Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 726588
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:2
Variant summary: HNF4A c.-18G>A is located in the untranslated mRNA region upstream of the initiation codon. The variant was absent in 246952 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-18G>A in individuals affected with maturity onset diabetes of the Young 1/neonatal diabetes mellitus and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1337492). Based on the evidence outlined above, the variant was classified as uncertain significance. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at