rs1890908

Variant summary

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

The NM_182914.3(SYNE2):​c.8404A>C​(p.Ser2802Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S2802G) has been classified as Benign.

Frequency

Genomes: not found (cov: 32)

Consequence

SYNE2
NM_182914.3 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.59
Variant links:
Genes affected
SYNE2 (HGNC:17084): (spectrin repeat containing nuclear envelope protein 2) The protein encoded by this gene is a nuclear outer membrane protein that binds cytoplasmic F-actin. This binding tethers the nucleus to the cytoskeleton and aids in the maintenance of the structural integrity of the nucleus. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

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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;
BP4
Computational evidence support a benign effect (MetaRNN=0.068701446).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SYNE2NM_182914.3 linkuse as main transcriptc.8404A>C p.Ser2802Arg missense_variant 48/116 ENST00000555002.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SYNE2ENST00000555002.6 linkuse as main transcriptc.8404A>C p.Ser2802Arg missense_variant 48/1161 NM_182914.3 P4Q8WXH0-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
71
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.17
BayesDel_addAF
Benign
-0.26
T
BayesDel_noAF
Benign
-0.62
CADD
Benign
0.023
DANN
Benign
0.81
DEOGEN2
Benign
0.031
.;T;T;T
Eigen
Benign
-1.8
Eigen_PC
Benign
-1.8
FATHMM_MKL
Benign
0.036
N
LIST_S2
Benign
0.66
T;T;T;T
M_CAP
Benign
0.013
T
MetaRNN
Benign
0.069
T;T;T;T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.0
L;.;L;.
MutationTaster
Benign
1.0
P;P;P;P
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-1.8
N;.;N;N
REVEL
Benign
0.011
Sift
Benign
0.045
D;.;T;D
Sift4G
Uncertain
0.016
D;D;D;D
Polyphen
0.23
B;.;B;.
Vest4
0.14
MutPred
0.21
Gain of catalytic residue at S2802 (P = 0.0326);.;Gain of catalytic residue at S2802 (P = 0.0326);.;
MVP
0.076
MPC
0.076
ClinPred
0.15
T
GERP RS
-6.9
Varity_R
0.12
gMVP
0.13

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: rs1890908; hg19: chr14-64519035; API