3-50270239-T-C
Position:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_001290060.2(SEMA3B):āc.222T>Cā(p.His74=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,460,774 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Genomes: not found (cov: 33)
Exomes š: 0.000032 ( 0 hom. )
Consequence
SEMA3B
NM_001290060.2 synonymous
NM_001290060.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.777
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
Variant 3-50270239-T-C is Benign according to our data. Variant chr3-50270239-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 3051968.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-0.777 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA3B | NM_001290060.2 | c.222T>C | p.His74= | synonymous_variant | 2/17 | ENST00000616701.5 | |
SEMA3B | NM_001290061.1 | c.222T>C | p.His74= | synonymous_variant | 2/17 | ||
SEMA3B | NM_004636.4 | c.222T>C | p.His74= | synonymous_variant | 3/18 | ||
SEMA3B | NM_001005914.3 | c.222T>C | p.His74= | synonymous_variant | 3/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA3B | ENST00000616701.5 | c.222T>C | p.His74= | synonymous_variant | 2/17 | 1 | NM_001290060.2 | P5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 genomes
Cov.:
33
GnomAD3 exomes AF: 0.0000324 AC: 8AN: 247004Hom.: 0 AF XY: 0.0000373 AC XY: 5AN XY: 134212
GnomAD3 exomes
AF:
AC:
8
AN:
247004
Hom.:
AF XY:
AC XY:
5
AN XY:
134212
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1460774Hom.: 0 Cov.: 32 AF XY: 0.0000385 AC XY: 28AN XY: 726612
GnomAD4 exome
AF:
AC:
47
AN:
1460774
Hom.:
Cov.:
32
AF XY:
AC XY:
28
AN XY:
726612
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 33
GnomAD4 genome
Cov.:
33
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SEMA3B-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 11, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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