chr11-27125777-C-A
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_003986.3(BBOX1):c.960C>A(p.Leu320=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00328 in 1,613,042 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0019 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0034 ( 9 hom. )
Consequence
BBOX1
NM_003986.3 synonymous
NM_003986.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.307
Genes affected
BBOX1 (HGNC:964): (gamma-butyrobetaine hydroxylase 1) This gene encodes gamma butyrobetaine hydroxylase which catalyzes the formation of L-carnitine from gamma-butyrobetaine, the last step in the L-carnitine biosynthetic pathway. Carnitine is essential for the transport of activated fatty acids across the mitochondrial membrane during mitochondrial beta-oxidation. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.31).
BP6
Variant 11-27125777-C-A is Benign according to our data. Variant chr11-27125777-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 3035182.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.307 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 9 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BBOX1 | NM_003986.3 | c.960C>A | p.Leu320= | synonymous_variant | 8/9 | ENST00000263182.8 | |
BBOX1-AS1 | NR_125768.1 | n.377+25273G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BBOX1 | ENST00000263182.8 | c.960C>A | p.Leu320= | synonymous_variant | 8/9 | 5 | NM_003986.3 | P1 | |
BBOX1-AS1 | ENST00000526061.5 | n.344+25273G>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00189 AC: 288AN: 152158Hom.: 1 Cov.: 32
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GnomAD3 exomes AF: 0.00227 AC: 562AN: 247860Hom.: 4 AF XY: 0.00247 AC XY: 332AN XY: 134150
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GnomAD4 exome AF: 0.00342 AC: 4996AN: 1460766Hom.: 9 Cov.: 31 AF XY: 0.00340 AC XY: 2469AN XY: 726610
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GnomAD4 genome AF: 0.00189 AC: 288AN: 152276Hom.: 1 Cov.: 32 AF XY: 0.00180 AC XY: 134AN XY: 74450
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
BBOX1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 25, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
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DANN
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at