7-27543085-C-A
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_152740.4(HIBADH):c.500G>T(p.Arg167Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000254 in 1,613,582 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
HIBADH
NM_152740.4 missense
NM_152740.4 missense
Scores
2
6
11
Clinical Significance
Conservation
PhyloP100: 3.99
Genes affected
HIBADH (HGNC:4907): (3-hydroxyisobutyrate dehydrogenase) This gene encodes a mitochondrial 3-hydroxyisobutyrate dehydrogenase enzyme. The encoded protein plays a critical role in the catabolism of L-valine by catalyzing the oxidation of 3-hydroxyisobutyrate to methylmalonate semialdehyde. [provided by RefSeq, Nov 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIBADH | NM_152740.4 | c.500G>T | p.Arg167Leu | missense_variant | 5/8 | ENST00000265395.7 | |
HIBADH | XM_047419834.1 | c.197G>T | p.Arg66Leu | missense_variant | 4/7 | ||
HIBADH | XM_047419835.1 | c.197G>T | p.Arg66Leu | missense_variant | 4/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIBADH | ENST00000265395.7 | c.500G>T | p.Arg167Leu | missense_variant | 5/8 | 1 | NM_152740.4 | P1 | |
HIBADH | ENST00000425715.1 | c.329G>T | p.Arg110Leu | missense_variant | 4/6 | 2 | |||
HIBADH | ENST00000428288.2 | c.*219G>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/7 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152136Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250736Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135488
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GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461446Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727000
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GnomAD4 genome AF: 0.0000986 AC: 15AN: 152136Hom.: 0 Cov.: 31 AF XY: 0.000135 AC XY: 10AN XY: 74320
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 14, 2024 | The c.500G>T (p.R167L) alteration is located in exon 5 (coding exon 5) of the HIBADH gene. This alteration results from a G to T substitution at nucleotide position 500, causing the arginine (R) at amino acid position 167 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Uncertain
T
Eigen
Benign
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Benign
D
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at