3-50269320-GC-GCC
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001290061.1(SEMA3B):c.86dupC(p.Arg30ThrfsTer33) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
SEMA3B
NM_001290061.1 frameshift
NM_001290061.1 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0550
Publications
10 publications found
Genes affected
SEMA3B (HGNC:10724): (semaphorin 3B) The protein encoded by this gene belongs to the class-3 semaphorin/collapsin family, whose members function in growth cone guidance during neuronal development. This family member inhibits axonal extension and has been shown to act as a tumor suppressor by inducing apoptosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2014]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 3-50269320-G-GC is Benign according to our data. Variant chr3-50269320-G-GC is described in ClinVar as Benign. ClinVar VariationId is 3060238.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_001290061.1. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SEMA3B | NM_001290060.2 | MANE Select | c.86dupC | p.Arg30ThrfsTer33 | frameshift | Exon 1 of 17 | NP_001276989.1 | ||
| SEMA3B | NM_001290061.1 | c.86dupC | p.Arg30ThrfsTer33 | frameshift | Exon 1 of 17 | NP_001276990.1 | |||
| SEMA3B | NM_001435956.1 | c.86dupC | p.Arg30ThrfsTer33 | frameshift | Exon 4 of 20 | NP_001422885.1 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SEMA3B | ENST00000616701.5 | TSL:1 MANE Select | c.86dupC | p.Arg30ThrfsTer33 | frameshift | Exon 1 of 17 | ENSP00000484146.1 | ||
| SEMA3B | ENST00000611067.4 | TSL:1 | c.86dupC | p.Arg30ThrfsTer33 | frameshift | Exon 1 of 17 | ENSP00000480680.1 | ||
| SEMA3B | ENST00000433753.4 | TSL:1 | c.86dupC | p.Arg30ThrfsTer33 | frameshift | Exon 1 of 17 | ENSP00000485281.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 1.00 AC: 111467AN: 111490 AF XY: 1.00 show subpopulations
GnomAD2 exomes
AF:
AC:
111467
AN:
111490
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1364122Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 672962
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1364122
Hom.:
Cov.:
30
AF XY:
AC XY:
0
AN XY:
672962
African (AFR)
AF:
AC:
0
AN:
29840
American (AMR)
AF:
AC:
0
AN:
27942
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
23568
East Asian (EAS)
AF:
AC:
0
AN:
35530
South Asian (SAS)
AF:
AC:
0
AN:
76168
European-Finnish (FIN)
AF:
AC:
0
AN:
39402
Middle Eastern (MID)
AF:
AC:
0
AN:
5220
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1069882
Other (OTH)
AF:
AC:
0
AN:
56570
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Asia WGS
AF:
AC:
3478
AN:
3478
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
SEMA3B-related disorder (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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