chr11-27125747-T-C
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_003986.3(BBOX1):āc.930T>Cā(p.Phe310=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00473 in 1,613,864 control chromosomes in the GnomAD database, including 190 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.019 ( 86 hom., cov: 32)
Exomes š: 0.0033 ( 104 hom. )
Consequence
BBOX1
NM_003986.3 synonymous
NM_003986.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.365
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 -15 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 11-27125747-T-C is Benign according to our data. Variant chr11-27125747-T-C is described in ClinVar as [Benign]. Clinvar id is 778515.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.365 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0596 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BBOX1 | NM_003986.3 | c.930T>C | p.Phe310= | synonymous_variant | 8/9 | ENST00000263182.8 | |
BBOX1-AS1 | NR_125768.1 | n.377+25303A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BBOX1 | ENST00000263182.8 | c.930T>C | p.Phe310= | synonymous_variant | 8/9 | 5 | NM_003986.3 | P1 | |
BBOX1-AS1 | ENST00000526061.5 | n.344+25303A>G | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0190 AC: 2884AN: 152146Hom.: 87 Cov.: 32
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GnomAD3 exomes AF: 0.00688 AC: 1709AN: 248554Hom.: 37 AF XY: 0.00549 AC XY: 739AN XY: 134568
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GnomAD4 exome AF: 0.00325 AC: 4754AN: 1461600Hom.: 104 Cov.: 31 AF XY: 0.00303 AC XY: 2201AN XY: 727096
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GnomAD4 genome AF: 0.0189 AC: 2882AN: 152264Hom.: 86 Cov.: 32 AF XY: 0.0181 AC XY: 1349AN XY: 74456
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2018 | - - |
Computational scores
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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