X-48354677-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate

The NM_021014.4(SSX3):​c.139G>A​(p.Val47Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000746 in 1,206,031 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V47A) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.000027 ( 0 hom., 1 hem., cov: 22)
Exomes 𝑓: 0.0000055 ( 0 hom. 0 hem. )

Consequence

SSX3
NM_021014.4 missense

Scores

1
16

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.278
Variant links:
Genes affected
SSX3 (HGNC:11337): (SSX family member 3) 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. [provided by RefSeq, Jul 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.036298364).
BP6
Variant X-48354677-C-T is Benign according to our data. Variant chrX-48354677-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3322904.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SSX3NM_021014.4 linkc.139G>A p.Val47Ile missense_variant Exon 3 of 8 ENST00000298396.7 NP_066294.1 Q99909-1
SSX3XM_011543885.3 linkc.139G>A p.Val47Ile missense_variant Exon 3 of 7 XP_011542187.1 Q99909-2A0A024R1B1
SSX3NR_176964.1 linkn.229G>A non_coding_transcript_exon_variant Exon 3 of 9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SSX3ENST00000298396.7 linkc.139G>A p.Val47Ile missense_variant Exon 3 of 8 1 NM_021014.4 ENSP00000298396.2 Q99909-1
SSX3ENST00000612497.1 linkc.139G>A p.Val47Ile missense_variant Exon 2 of 5 5 ENSP00000480427.1 A0A087WWQ6
SSX3ENST00000376893.7 linkc.139G>A p.Val47Ile missense_variant Exon 3 of 8 2 ENSP00000366090.3 Q99909-2

Frequencies

GnomAD3 genomes
AF:
0.0000273
AC:
3
AN:
110069
Hom.:
0
Cov.:
22
AF XY:
0.0000309
AC XY:
1
AN XY:
32361
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:
0.0000568
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000164
AC:
3
AN:
182972
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
67564
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:
0.0000527
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000245
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000547
AC:
6
AN:
1095962
Hom.:
0
Cov.:
30
AF XY:
0.00
AC XY:
0
AN XY:
361664
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000185
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000595
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000273
AC:
3
AN:
110069
Hom.:
0
Cov.:
22
AF XY:
0.0000309
AC XY:
1
AN XY:
32361
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:
0.0000568
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000189
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
May 20, 2024
Ambry Genetics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.082
BayesDel_addAF
Benign
-0.65
T
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.13
DANN
Benign
0.72
DEOGEN2
Benign
0.0067
T;.;.
FATHMM_MKL
Benign
0.00051
N
LIST_S2
Benign
0.029
T;T;T
M_CAP
Benign
0.00086
T
MetaRNN
Benign
0.036
T;T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
-0.55
N;N;.
PrimateAI
Uncertain
0.49
T
PROVEAN
Benign
-0.22
N;N;.
REVEL
Benign
0.0040
Sift
Benign
0.46
T;T;.
Sift4G
Benign
0.69
T;T;T
Polyphen
0.0
B;.;.
Vest4
0.017
MutPred
0.32
Loss of loop (P = 0.1242);Loss of loop (P = 0.1242);Loss of loop (P = 0.1242);
MVP
0.076
MPC
0.020
ClinPred
0.045
T
GERP RS
-3.5
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Varity_R
0.030
gMVP
0.041

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: rs781910604; hg19: chrX-48214112; API