12-120978645-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_000545.8(HNF1A):c.-124G>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 0.0000863 in 926,554 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_000545.8 5_prime_UTR
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 |
---|---|---|---|---|---|---|---|---|
HNF1A | NM_000545.8 | c.-124G>A | 5_prime_UTR_variant | Exon 1 of 10 | ENST00000257555.11 | NP_000536.6 | ||
HNF1A | NM_001306179.2 | c.-124G>A | 5_prime_UTR_variant | Exon 1 of 10 | NP_001293108.2 | |||
HNF1A | NM_001406915.1 | c.-124G>A | 5_prime_UTR_variant | Exon 1 of 9 | NP_001393844.1 | |||
HNF1A | XM_024449168.2 | c.-124G>A | 5_prime_UTR_variant | Exon 1 of 9 | XP_024304936.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HNF1A | ENST00000257555 | c.-124G>A | 5_prime_UTR_variant | Exon 1 of 10 | 1 | NM_000545.8 | ENSP00000257555.5 |
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 6AN: 188332Hom.: 0 AF XY: 0.0000379 AC XY: 4AN XY: 105640
GnomAD4 exome AF: 0.0000878 AC: 68AN: 774312Hom.: 0 Cov.: 11 AF XY: 0.0000829 AC XY: 34AN XY: 409910
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74444
ClinVar
Submissions by phenotype
not provided Uncertain:2
This variant occurs in a non-coding region of the HNF1A gene. It does not change the encoded amino acid sequence of the HNF1A protein. This variant is present in population databases (rs563304627, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with HNF1A-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at