1-84656457-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001166293.2(SSX2IP):​c.1106A>G​(p.Asn369Ser) 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. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

SSX2IP
NM_001166293.2 missense

Scores

1
18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.641
Variant links:
Genes affected
SSX2IP (HGNC:16509): (SSX family member 2 interacting protein) This gene encodes a protein that binds the cancer-testis antigen Synovial Sarcoma X breakpoint 2 protein. The encoded protein may regulate the activity of Synovial Sarcoma X breakpoint 2 protein in malignant cells. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Oct 2009]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.05713886).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SSX2IPNM_001166293.2 linkc.1106A>G p.Asn369Ser missense_variant 10/14 ENST00000342203.8 NP_001159765.1 Q9Y2D8-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SSX2IPENST00000342203.8 linkc.1106A>G p.Asn369Ser missense_variant 10/141 NM_001166293.2 ENSP00000340279.3 Q9Y2D8-1
SSX2IPENST00000476905.6 linkn.1094A>G non_coding_transcript_exon_variant 11/162 ENSP00000474925.1 S4R403

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsNov 10, 2022The c.1106A>G (p.N369S) alteration is located in exon 11 (coding exon 9) of the SSX2IP gene. This alteration results from a A to G substitution at nucleotide position 1106, causing the asparagine (N) at amino acid position 369 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.059
BayesDel_addAF
Benign
-0.32
T
BayesDel_noAF
Benign
-0.70
CADD
Benign
5.1
DANN
Uncertain
0.98
DEOGEN2
Benign
0.050
.;T;.
Eigen
Benign
-0.62
Eigen_PC
Benign
-0.58
FATHMM_MKL
Benign
0.46
N
LIST_S2
Benign
0.77
T;T;.
M_CAP
Benign
0.0073
T
MetaRNN
Benign
0.057
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.95
.;L;.
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-1.4
N;N;.
REVEL
Benign
0.035
Sift
Benign
0.11
T;T;.
Sift4G
Benign
0.70
T;T;T
Polyphen
0.0020
.;B;.
Vest4
0.12
MutPred
0.17
.;Gain of phosphorylation at N369 (P = 0.0424);.;
MVP
0.24
MPC
0.056
ClinPred
0.085
T
GERP RS
2.0
Varity_R
0.029
gMVP
0.065

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: rs1651139952; hg19: chr1-85122140; API