rs782033607

Variant names:

• chrX-48194170-T-A
• NM_175723.2:c.239A>T

Your query was ambiguous. Multiple possible variants found:

• chrX-48194170-T-A
• chrX-48194170-T-C
• chrX-48194170-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_175723.2(SSX5):​c.239A>T​(p.Gln80Leu) 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. 12/20 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. Q80H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 21)
• Consequence: SSX5 NM_175723.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

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]

ACMG classification

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=0.16058078).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSX5	NM_175723.2	c.239A>T	p.Gln80Leu	missense_variant	Exon 4 of 8	ENST00000347757.6	NP_783729.1
SSX5	NM_021015.4	c.362A>T	p.Gln121Leu	missense_variant	Exon 5 of 9		NP_066295.3
SSX5	XM_011543949.3	c.239A>T	p.Gln80Leu	missense_variant	Exon 4 of 8		XP_011542251.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSX5	ENST00000347757.6	c.239A>T	p.Gln80Leu	missense_variant	Exon 4 of 8	5	NM_175723.2	ENSP00000290558.1
SSX5	ENST00000311798.5	c.362A>T	p.Gln121Leu	missense_variant	Exon 5 of 9	5		ENSP00000312415.1

Frequencies

GnomAD3 genomes Cov.: 21

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 21

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.46	T
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.96
DEOGEN2	Benign	0.073	T;.;T
FATHMM_MKL	Benign	0.0020	N
LIST_S2	Benign	0.84	.;T;T
M_CAP	Benign	0.0085	T
MetaRNN	Benign	0.16	T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Uncertain	2.7	M;.;M
PrimateAI	Benign	0.22	T
PROVEAN	Uncertain	-3.7	D;D;D
REVEL	Benign	0.087
Sift	Uncertain	0.0040	D;D;D
Sift4G	Uncertain	0.011	D;D;D
Polyphen		0.77	P;P;P
Vest4		0.23
MutPred		0.28		Loss of disorder (P = 0.0297);.;Loss of disorder (P = 0.0297);
MVP		0.067
MPC		0.033
ClinPred		0.78	D
GERP RS		-3.4
Varity_R		0.097
gMVP		0.046

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

No publications associated with this variant yet.

Other links and lift over

hg19: chrX-48053606;