1-42816516-GT-GTT
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 4P and 4B. PVS1_StrongBS2
The NM_199342.4(SVBP):c.28dupA(p.Thr10AsnfsTer4) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,772 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
SVBP
NM_199342.4 frameshift
NM_199342.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0200
Publications
0 publications found
Genes affected
SVBP (HGNC:29204): (small vasohibin binding protein) Enables microtubule binding activity. Involved in axon development; proteolysis; and regulation of metallopeptidase activity. Acts upstream of or within negative regulation of endothelial cell migration; negative regulation of protein ubiquitination; and protein secretion. Located in apical part of cell. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 5 pathogenic variants in the truncated region.
BS2
High AC in GnomAdExome4 at 8 AD gene.
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| SVBP | ENST00000372521.9 | c.28dupA | p.Thr10AsnfsTer4 | frameshift_variant | Exon 2 of 3 | 1 | NM_199342.4 | ENSP00000361599.4 | ||
| SVBP | ENST00000372522.5 | c.28dupA | p.Thr10AsnfsTer4 | frameshift_variant | Exon 2 of 3 | 3 | ENSP00000361600.1 | |||
| SVBP | ENST00000497437.1 | n.127dupA | non_coding_transcript_exon_variant | Exon 2 of 3 | 3 | |||||
| TMEM269 | ENST00000421630.6 | n.*424-13dupT | intron_variant | Intron 10 of 10 | 5 | ENSP00000490287.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461772Hom.: 0 Cov.: 30 AF XY: 0.00000550 AC XY: 4AN XY: 727184 show subpopulations
GnomAD4 exome
AF:
AC:
8
AN:
1461772
Hom.:
Cov.:
30
AF XY:
AC XY:
4
AN XY:
727184
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33474
American (AMR)
AF:
AC:
0
AN:
44716
Ashkenazi Jewish (ASJ)
AF:
AC:
3
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39678
South Asian (SAS)
AF:
AC:
0
AN:
86244
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5766
European-Non Finnish (NFE)
AF:
AC:
5
AN:
1111946
Other (OTH)
AF:
AC:
0
AN:
60392
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.488
Heterozygous variant carriers
0
1
2
2
3
4
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
Dec 01, 2017
CeGaT Center for Human Genetics Tuebingen
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
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Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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