3-50269248-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001290060.2(SEMA3B):​c.8G>A​(p.Arg3Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000173 in 1,383,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 9/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.000017 ( 0 hom. )

Consequence

SEMA3B
NM_001290060.2 missense

Scores

1
12

Clinical Significance

Uncertain significance no assertion criteria provided U:1

Conservation

PhyloP100: 0.212
Variant links:
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 Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.12006864).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SEMA3BNM_001290060.2 linkc.8G>A p.Arg3Gln missense_variant 1/17 ENST00000616701.5 NP_001276989.1 Q13214-1
SEMA3BNM_001290061.1 linkc.8G>A p.Arg3Gln missense_variant 1/17 NP_001276990.1 Q13214A0A0C4DGV8
SEMA3BNM_004636.4 linkc.8G>A p.Arg3Gln missense_variant 2/18 NP_004627.1 Q13214-1
SEMA3BNM_001005914.3 linkc.8G>A p.Arg3Gln missense_variant 2/18 NP_001005914.1 Q13214-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SEMA3BENST00000616701.5 linkc.8G>A p.Arg3Gln missense_variant 1/171 NM_001290060.2 ENSP00000484146.1 Q13214-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD3 exomes
AF:
0.0000148
AC:
2
AN:
134770
Hom.:
0
AF XY:
0.0000137
AC XY:
1
AN XY:
73072
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000816
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000173
AC:
24
AN:
1383834
Hom.:
0
Cov.:
31
AF XY:
0.0000249
AC XY:
17
AN XY:
683030
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000841
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000280
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000185
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

SEMA3B-related disorder Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesAug 23, 2024The SEMA3B c.8G>A variant is predicted to result in the amino acid substitution p.Arg3Gln. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0082% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.0072
T
BayesDel_noAF
Benign
-0.25
CADD
Benign
16
DANN
Benign
0.88
DEOGEN2
Benign
0.056
.;T;T;.;.
Eigen
Benign
-0.51
Eigen_PC
Benign
-0.47
FATHMM_MKL
Benign
0.62
D
LIST_S2
Benign
0.73
T;T;.;T;T
MetaRNN
Benign
0.12
T;T;T;T;T
MetaSVM
Benign
-0.93
T
PrimateAI
Uncertain
0.59
T
Sift4G
Benign
0.13
T;T;T;T;T
Polyphen
0.0060
.;B;B;.;.
Vest4
0.081, 0.077, 0.093, 0.16
MutPred
0.36
Loss of methylation at R3 (P = 0.0011);Loss of methylation at R3 (P = 0.0011);Loss of methylation at R3 (P = 0.0011);Loss of methylation at R3 (P = 0.0011);Loss of methylation at R3 (P = 0.0011);
MVP
0.17
ClinPred
0.19
T
GERP RS
3.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.043
gMVP
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1553704920; hg19: chr3-50306680; API