rs1555589
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_206808.5(CLYBL):c.250-30451G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 152,188 control chromosomes in the GnomAD database, including 45,345 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.76 ( 45345 hom., cov: 33)
Consequence
CLYBL
NM_206808.5 intron
NM_206808.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.713
Genes affected
CLYBL (HGNC:18355): (citramalyl-CoA lyase) Enables (S)-citramalyl-CoA lyase activity; magnesium ion binding activity; and malate synthase activity. Involved in protein homotrimerization and regulation of cobalamin metabolic process. Predicted to be located in mitochondrion. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.64).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.927 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLYBL | NM_206808.5 | c.250-30451G>A | intron_variant | ENST00000339105.9 | |||
CLYBL-AS3 | NR_120421.1 | n.84-53062C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLYBL | ENST00000339105.9 | c.250-30451G>A | intron_variant | 1 | NM_206808.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.761 AC: 115768AN: 152070Hom.: 45298 Cov.: 33
GnomAD3 genomes
?
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115768
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152070
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.761 AC: 115872AN: 152188Hom.: 45345 Cov.: 33 AF XY: 0.763 AC XY: 56730AN XY: 74396
GnomAD4 genome
?
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AC:
115872
AN:
152188
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33
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56730
AN XY:
74396
Gnomad4 AFR
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Asia WGS
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2907
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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