1-208028046-T-C

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_025179.4(PLXNA2):ā€‹c.5552A>Gā€‹(p.Asn1851Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000553 in 1,608,776 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000092 ( 0 hom., cov: 33)
Exomes š‘“: 0.000051 ( 0 hom. )

Consequence

PLXNA2
NM_025179.4 missense

Scores

3
16

Clinical Significance

Uncertain significance criteria provided, single submitter U:2

Conservation

PhyloP100: 4.01
Variant links:
Genes affected
PLXNA2 (HGNC:9100): (plexin A2) This gene encodes a member of the plexin-A family of semaphorin co-receptors. Semaphorins are a large family of secreted or membrane-bound proteins that mediate repulsive effects on axon pathfinding during nervous system development. A subset of semaphorins are recognized by plexin-A/neuropilin transmembrane receptor complexes, triggering a cellular signal transduction cascade that leads to axon repulsion. This plexin-A family member is thought to transduce signals from semaphorin-3A and -3C. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.15440306).
BS2
High AC in GnomAd4 at 14 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PLXNA2NM_025179.4 linkuse as main transcriptc.5552A>G p.Asn1851Ser missense_variant 31/32 ENST00000367033.4 NP_079455.3 O75051-1
PLXNA2XM_005273164.4 linkuse as main transcriptc.5792A>G p.Asn1931Ser missense_variant 32/33 XP_005273221.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PLXNA2ENST00000367033.4 linkuse as main transcriptc.5552A>G p.Asn1851Ser missense_variant 31/321 NM_025179.4 ENSP00000356000.3 O75051-1
PLXNA2ENST00000483048.1 linkuse as main transcriptn.1588A>G non_coding_transcript_exon_variant 2/31

Frequencies

GnomAD3 genomes
AF:
0.0000923
AC:
14
AN:
151712
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000192
Gnomad OTH
AF:
0.000480
GnomAD3 exomes
AF:
0.0000402
AC:
10
AN:
248676
Hom.:
0
AF XY:
0.0000446
AC XY:
6
AN XY:
134414
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000296
Gnomad ASJ exome
AF:
0.000100
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000708
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000515
AC:
75
AN:
1457064
Hom.:
0
Cov.:
31
AF XY:
0.0000483
AC XY:
35
AN XY:
724786
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.000192
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000234
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.0000559
Gnomad4 OTH exome
AF:
0.0000831
GnomAD4 genome
AF:
0.0000923
AC:
14
AN:
151712
Hom.:
0
Cov.:
33
AF XY:
0.0000540
AC XY:
4
AN XY:
74104
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000192
Gnomad4 OTH
AF:
0.000480
Alfa
AF:
0.000249
Hom.:
0
Bravo
AF:
0.0000718
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.00
AC:
0
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.0000330
AC:
4
EpiCase
AF:
0.0000549
EpiControl
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpOct 25, 2022In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt PLXNA2 protein function. This variant has not been reported in the literature in individuals affected with PLXNA2-related conditions. This variant is present in population databases (rs141837222, gnomAD 0.01%). This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 1851 of the PLXNA2 protein (p.Asn1851Ser). -
PLXNA2-related disorder Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMay 17, 2024The PLXNA2 c.5552A>G variant is predicted to result in the amino acid substitution p.Asn1851Ser. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.011% of alleles in individuals of European (Non-Finnish) 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
0.072
BayesDel_addAF
Benign
-0.45
T
BayesDel_noAF
Benign
-0.57
CADD
Benign
19
DANN
Benign
0.90
DEOGEN2
Benign
0.076
T
Eigen
Benign
-0.51
Eigen_PC
Benign
-0.25
FATHMM_MKL
Uncertain
0.94
D
LIST_S2
Uncertain
0.86
D
M_CAP
Benign
0.0045
T
MetaRNN
Benign
0.15
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-0.68
N
PrimateAI
Uncertain
0.58
T
PROVEAN
Benign
-0.66
N
REVEL
Benign
0.069
Sift
Benign
0.95
T
Sift4G
Benign
0.60
T
Polyphen
0.0090
B
Vest4
0.26
MVP
0.44
MPC
0.47
ClinPred
0.091
T
GERP RS
4.4
Varity_R
0.076
gMVP
0.37

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.16
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: rs141837222; hg19: chr1-208201391; API