chr2-190205025-G-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_014362.4(HIBCH):c.*92C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00323 in 726,598 control chromosomes in the GnomAD database, including 32 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.010 ( 22 hom., cov: 32)
Exomes 𝑓: 0.0013 ( 10 hom. )
Consequence
HIBCH
NM_014362.4 3_prime_UTR
NM_014362.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.373
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 2-190205025-G-C is Benign according to our data. Variant chr2-190205025-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 1321705.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0105 (1595/152238) while in subpopulation AFR AF= 0.0368 (1528/41536). AF 95% confidence interval is 0.0353. There are 22 homozygotes in gnomad4. There are 772 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 22 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HIBCH | NM_014362.4 | c.*92C>G | 3_prime_UTR_variant | 14/14 | ENST00000359678.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HIBCH | ENST00000359678.10 | c.*92C>G | 3_prime_UTR_variant | 14/14 | 1 | NM_014362.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0104 AC: 1588AN: 152122Hom.: 22 Cov.: 32
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GnomAD4 exome AF: 0.00131 AC: 752AN: 574360Hom.: 10 Cov.: 6 AF XY: 0.00102 AC XY: 316AN XY: 310160
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GnomAD4 genome ? AF: 0.0105 AC: 1595AN: 152238Hom.: 22 Cov.: 32 AF XY: 0.0104 AC XY: 772AN XY: 74446
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 12, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at