20-58389302-AC-ACCCCC
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_004738.5(VAPB):c.-152_-149dupCCCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0 ( 0 hom., cov: 27)
Exomes 𝑓: 0.000015 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
VAPB
NM_004738.5 5_prime_UTR
NM_004738.5 5_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.452
Genes affected
VAPB (HGNC:12649): (VAMP associated protein B and C) The protein encoded by this gene is a type IV membrane protein found in plasma and intracellular vesicle membranes. The encoded protein is found as a homodimer and as a heterodimer with VAPA. This protein also can interact with VAMP1 and VAMP2 and may be involved in vesicle trafficking. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VAPB | NM_004738.5 | c.-152_-149dupCCCC | 5_prime_UTR_variant | Exon 1 of 6 | ENST00000475243.6 | NP_004729.1 | ||
VAPB | NM_001195677.2 | c.-152_-149dupCCCC | 5_prime_UTR_variant | Exon 1 of 3 | NP_001182606.1 | |||
VAPB | NR_036633.2 | n.80_83dupCCCC | non_coding_transcript_exon_variant | Exon 1 of 4 | ||||
VAPB | XR_001754433.3 | n.80_83dupCCCC | non_coding_transcript_exon_variant | Exon 1 of 6 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 128504Hom.: 0 Cov.: 27 FAILED QC
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GnomAD3 exomes AF: 0.0000147 AC: 1AN: 67844Hom.: 0 AF XY: 0.0000265 AC XY: 1AN XY: 37796
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GnomAD4 exome AF: 0.0000147 AC: 4AN: 271602Hom.: 0 Cov.: 5 AF XY: 0.0000194 AC XY: 3AN XY: 154570
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GnomAD4 genome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 128504Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 61714
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at