3-50269320-G-GC
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_001290060.2(SEMA3B):c.86dup(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_001290060.2 frameshift
NM_001290060.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.0550
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 made for transcript
Verdict is Uncertain_significance. Variant got 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 id is 3060238.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| SEMA3B | NM_001290060.2 | c.86dup | p.Arg30ThrfsTer33 | frameshift_variant | 1/17 | ENST00000616701.5 | |
| SEMA3B | NM_001005914.3 | c.86dup | p.Arg30ThrfsTer33 | frameshift_variant | 2/18 | ||
| SEMA3B | NM_001290061.1 | c.86dup | p.Arg30ThrfsTer33 | frameshift_variant | 1/17 | ||
| SEMA3B | NM_004636.4 | c.86dup | p.Arg30ThrfsTer33 | frameshift_variant | 2/18 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| SEMA3B | ENST00000616701.5 | c.86dup | p.Arg30ThrfsTer33 | frameshift_variant | 1/17 | 1 | NM_001290060.2 | P5 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 1.00 AC: 111467AN: 111490Hom.: 55722 AF XY: 1.00 AC XY: 61447AN XY: 61458
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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
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GnomAD4 genome
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
SEMA3B-related disorder Benign:1
| Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 17, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at