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

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.452
Variant links:
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]

Genome browser will be placed here

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
VAPBNM_004738.5 linkc.-152_-149dupCCCC 5_prime_UTR_variant Exon 1 of 6 ENST00000475243.6 NP_004729.1 O95292-1Q53XM7
VAPBNM_001195677.2 linkc.-152_-149dupCCCC 5_prime_UTR_variant Exon 1 of 3 NP_001182606.1 O95292-2
VAPBNR_036633.2 linkn.80_83dupCCCC non_coding_transcript_exon_variant Exon 1 of 4
VAPBXR_001754433.3 linkn.80_83dupCCCC non_coding_transcript_exon_variant Exon 1 of 6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
VAPBENST00000475243 linkc.-152_-149dupCCCC 5_prime_UTR_variant Exon 1 of 6 1 NM_004738.5 ENSP00000417175.1 O95292-1
VAPBENST00000395802.7 linkc.-158_-157insCCCC upstream_gene_variant 1 ENSP00000379147.3 O95292-2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
128504
Hom.:
0
Cov.:
27
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000147
AC:
1
AN:
67844
Hom.:
0
AF XY:
0.0000265
AC XY:
1
AN XY:
37796
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.000216
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000147
AC:
4
AN:
271602
Hom.:
0
Cov.:
5
AF XY:
0.0000194
AC XY:
3
AN XY:
154570
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000190
Gnomad4 FIN exome
AF:
0.0000586
Gnomad4 NFE exome
AF:
0.00000698
Gnomad4 OTH exome
AF:
0.0000800
GnomAD4 genome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
128504
Hom.:
0
Cov.:
27
AF XY:
0.00
AC XY:
0
AN XY:
61714
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs546898989; hg19: chr20-56964358; API