chr2-190205155-GATT-G
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4_SupportingPP5_Moderate
The NM_014362.4(HIBCH):c.1120_1122del(p.Asn374del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
HIBCH
NM_014362.4 inframe_deletion
NM_014362.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.123
Genes affected
HIBCH (HGNC:4908): (3-hydroxyisobutyryl-CoA hydrolase) This gene encodes the enzyme responsible for hydrolysis of both HIBYL-CoA and beta-hydroxypropionyl-CoA. Mutations in this gene have been associated with 3-hyroxyisobutyryl-CoA hydrolase deficiency. Alternative splicing results in multiple transcript variants.[provided by RefSeq, May 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PM4
?
Nonframeshift variant in NON repetitive region in NM_014362.4. Strenght limited to Supporting due to length of the change: 1aa.
PP5
?
Variant 2-190205155-GATT-G is Pathogenic according to our data. Variant chr2-190205155-GATT-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 424194.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIBCH | NM_014362.4 | c.1120_1122del | p.Asn374del | inframe_deletion | 14/14 | ENST00000359678.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIBCH | ENST00000359678.10 | c.1120_1122del | p.Asn374del | inframe_deletion | 14/14 | 1 | NM_014362.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 03, 2017 | The c.1120_1122delAAT variant in the HIBCH gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1120_1122delAAT variant causes an in-frame deletion of one amnio acid, Asparagine 374, denoted p.Asn374del. The c.1120_1122delAAT variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). We interpret c.1120_1122delAAT as a likely pathogenic variant. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at