rs753611165
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_004738.5(VAPB):c.58+5G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000563 in 1,580,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_004738.5 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VAPB | NM_004738.5 | c.58+5G>A | splice_region_variant, intron_variant | ENST00000475243.6 | NP_004729.1 | |||
VAPB | NM_001195677.2 | c.58+5G>A | splice_region_variant, intron_variant | NP_001182606.1 | ||||
VAPB | NR_036633.2 | n.289+5G>A | splice_region_variant, intron_variant | |||||
VAPB | XR_001754433.3 | n.289+5G>A | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VAPB | ENST00000475243.6 | c.58+5G>A | splice_region_variant, intron_variant | 1 | NM_004738.5 | ENSP00000417175.1 | ||||
VAPB | ENST00000395802.7 | c.58+5G>A | splice_region_variant, intron_variant | 1 | ENSP00000379147.3 | |||||
VAPB | ENST00000265619.6 | n.143+5G>A | splice_region_variant, intron_variant | 2 | ||||||
VAPB | ENST00000520497.1 | n.58+5G>A | splice_region_variant, intron_variant | 2 | ENSP00000430426.1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000454 AC: 9AN: 198152Hom.: 0 AF XY: 0.0000465 AC XY: 5AN XY: 107474
GnomAD4 exome AF: 0.0000581 AC: 83AN: 1428384Hom.: 0 Cov.: 32 AF XY: 0.0000508 AC XY: 36AN XY: 708174
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74274
ClinVar
Submissions by phenotype
Amyotrophic lateral sclerosis type 8;C1854058:Adult-onset proximal spinal muscular atrophy, autosomal dominant Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 24, 2023 | This variant has not been reported in the literature in individuals affected with VAPB-related conditions. This variant is present in population databases (rs753611165, gnomAD 0.009%). This sequence change falls in intron 1 of the VAPB gene. It does not directly change the encoded amino acid sequence of the VAPB protein. It affects a nucleotide within the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 574276). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2021 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at