X-48187636-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2

The NM_175723.2(SSX5):​c.562G>C​(p.Glu188Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000663 in 1,207,119 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000036 ( 0 hom., 2 hem., cov: 23)
Exomes 𝑓: 0.000069 ( 0 hom. 25 hem. )

Consequence

SSX5
NM_175723.2 missense

Scores

4
13

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: -0.0480
Variant links:
Genes affected
SSX5 (HGNC:11339): (SSX family member 5) The product of this gene belongs to the family of highly homologous synovial sarcoma X (SSX) breakpoint proteins. These proteins may function as transcriptional repressors. They are also capable of eliciting spontaneous humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. While some of the related SSX genes are involved in t(X;18)(p11.2;q11.2) translocations that are characteristically found in all synovial sarcomas, this gene does not appear to be involved in such translocations. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.022824228).
BS2
High Hemizygotes in GnomAd4 at 2 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SSX5NM_175723.2 linkc.562G>C p.Glu188Gln missense_variant Exon 7 of 8 ENST00000347757.6 NP_783729.1 O60225-1
SSX5NM_021015.4 linkc.685G>C p.Glu229Gln missense_variant Exon 8 of 9 NP_066295.3 O60225-2
SSX5XM_011543949.3 linkc.562G>C p.Glu188Gln missense_variant Exon 7 of 8 XP_011542251.1 O60225-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SSX5ENST00000347757.6 linkc.562G>C p.Glu188Gln missense_variant Exon 7 of 8 5 NM_175723.2 ENSP00000290558.1 O60225-1
SSX5ENST00000311798.5 linkc.685G>C p.Glu229Gln missense_variant Exon 8 of 9 5 ENSP00000312415.1 O60225-2
SSX5ENST00000403001.3 linkn.382G>C non_coding_transcript_exon_variant Exon 3 of 4 5

Frequencies

GnomAD3 genomes
AF:
0.0000358
AC:
4
AN:
111746
Hom.:
0
Cov.:
23
AF XY:
0.0000589
AC XY:
2
AN XY:
33952
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:
0.00112
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000929
AC:
17
AN:
182957
Hom.:
0
AF XY:
0.000133
AC XY:
9
AN XY:
67547
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00123
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:
0.0000694
AC:
76
AN:
1095373
Hom.:
0
Cov.:
30
AF XY:
0.0000691
AC XY:
25
AN XY:
361911
show subpopulations
Gnomad4 AFR exome
AF:
0.0000380
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00245
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.0000218
GnomAD4 genome
AF:
0.0000358
AC:
4
AN:
111746
Hom.:
0
Cov.:
23
AF XY:
0.0000589
AC XY:
2
AN XY:
33952
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00112
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000264
ExAC
AF:
0.000115
AC:
14

ClinVar

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

Submissions by phenotype

not specified Uncertain:1
May 18, 2023
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.685G>C (p.E229Q) alteration is located in exon 8 (coding exon 7) of the SSX5 gene. This alteration results from a G to C substitution at nucleotide position 685, causing the glutamic acid (E) at amino acid position 229 to be replaced by a glutamine (Q). 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
0.17
BayesDel_addAF
Benign
-0.63
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
7.2
DANN
Uncertain
0.98
DEOGEN2
Benign
0.060
T;.;T;.
FATHMM_MKL
Benign
0.011
N
LIST_S2
Uncertain
0.87
.;D;D;D
M_CAP
Benign
0.0013
T
MetaRNN
Benign
0.023
T;T;T;T
MetaSVM
Benign
-0.97
T
MutationAssessor
Benign
1.5
L;.;L;.
PrimateAI
Benign
0.44
T
PROVEAN
Benign
-1.4
N;N;N;N
REVEL
Benign
0.039
Sift
Uncertain
0.0060
D;D;D;D
Sift4G
Uncertain
0.0080
D;D;D;D
Polyphen
1.0
D;D;D;.
Vest4
0.18
MutPred
0.46
Loss of solvent accessibility (P = 0.0174);.;Loss of solvent accessibility (P = 0.0174);.;
MVP
0.15
MPC
0.063
ClinPred
0.10
T
GERP RS
0.12
Varity_R
0.19
gMVP
0.042

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: rs150017866; hg19: chrX-48047072; COSMIC: COSV99043399; API