X-52645457-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_173358.2(SSX7):​c.553G>C​(p.Glu185Gln) 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. 11/19 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. E185K) has been classified as Benign.

Frequency

Genomes: not found (cov: 21)
Exomes š‘“: 0.0000018 ( 0 hom. 2 hem. )
Failed GnomAD Quality Control

Consequence

SSX7
NM_173358.2 missense

Scores

1
4
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.34
Variant links:
Genes affected
SSX7 (HGNC:19653): (SSX family member 7) 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 spontaneously humoral and cellular immune responses in cancer patients, and are potentially useful targets in cancer vaccine-based immunotherapy. SSX1, SSX2 and SSX4 genes have been involved in the t(X;18) translocation characteristically found in all synovial sarcomas. This gene appears not to be involved in this type of chromosome translocation. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.29521486).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SSX7NM_173358.2 linkc.553G>C p.Glu185Gln missense_variant Exon 7 of 8 ENST00000298181.6 NP_775494.1 Q7RTT5A0A024R019

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SSX7ENST00000298181.6 linkc.553G>C p.Glu185Gln missense_variant Exon 7 of 8 5 NM_173358.2 ENSP00000298181.5 Q7RTT5

Frequencies

GnomAD3 genomes
Cov.:
21
GnomAD3 exomes
AF:
0.0000117
AC:
2
AN:
170963
Hom.:
0
AF XY:
0.0000352
AC XY:
2
AN XY:
56893
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.000129
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.00000184
AC:
2
AN:
1084315
Hom.:
0
Cov.:
28
AF XY:
0.00000569
AC XY:
2
AN XY:
351535
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000332
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000247
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.37
BayesDel_addAF
Benign
-0.43
T
BayesDel_noAF
Benign
-0.85
CADD
Benign
20
DANN
Uncertain
0.99
DEOGEN2
Benign
0.11
T
FATHMM_MKL
Benign
0.0095
N
LIST_S2
Uncertain
0.91
D
M_CAP
Benign
0.0015
T
MetaRNN
Benign
0.30
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
2.0
M
PROVEAN
Benign
-1.9
N
REVEL
Benign
0.081
Sift
Uncertain
0.0070
D
Sift4G
Pathogenic
0.0
D
Polyphen
1.0
D
Vest4
0.33
MutPred
0.60
Gain of relative solvent accessibility (P = 0.1684);
MVP
0.030
MPC
0.085
ClinPred
0.40
T
GERP RS
0.54
Varity_R
0.80
gMVP
0.029

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: rs146891115; hg19: chrX-52674507; API