4-107989738-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000505878(HADH):c.-18A>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000934 in 599,342 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
ENST00000505878 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 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 |
---|---|---|---|---|---|---|---|---|---|---|
HADH | ENST00000505878 | c.-18A>T | 5_prime_UTR_variant | Exon 1 of 9 | 1 | ENSP00000425952.2 | ||||
HADH | ENST00000603302 | c.-195A>T | 5_prime_UTR_variant | Exon 1 of 9 | 1 | ENSP00000474560.1 | ||||
CYP2U1-AS1 | ENST00000658105.3 | n.-14T>A | upstream_gene_variant |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152108Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000190 AC: 6AN: 31640Hom.: 0 AF XY: 0.000185 AC XY: 3AN XY: 16246
GnomAD4 exome AF: 0.000103 AC: 46AN: 447116Hom.: 0 Cov.: 5 AF XY: 0.000106 AC XY: 25AN XY: 236014
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152226Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74422
ClinVar
Submissions by phenotype
Hyperinsulinemic hypoglycemia Benign:1
Potent mutations in HADH gene are associated with congenital hyperinsulinism, which leads to recurrent hypoglycemia. The condition is exacerbated by stress, fasting or excessive dietary protein. May respond well to diazoxide. However, the role of this particular variant rs886058979 in congenital hyperinsulinism is yet to be ascertained. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at