X-52645494-C-T

Variant names:

• chrX-52645494-C-T
• rs1342577940
• NM_173358.2:c.516G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4_Strong BP7 BS2

The NM_173358.2(SSX7):​c.516G>A​(p.Lys172Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000175 in 1,201,673 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0000093 (0 hom., 1 hem., cov: 21)
  • Exomes 𝑓: 0.000018 (0 hom. 5 hem.)
• Consequence: SSX7 NM_173358.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP7: Synonymous conserved (PhyloP=-0.031 with no splicing effect.
• BS2: High Hemizygotes in GnomAdExome4 at 5 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173358.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSX7	NM_173358.2	MANE Select	c.516G>A	p.Lys172Lys	synonymous	Exon 7 of 8	NP_775494.1	Q7RTT5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SSX7	ENST00000298181.6	TSL:5 MANE Select	c.516G>A	p.Lys172Lys	synonymous	Exon 7 of 8	ENSP00000298181.5	Q7RTT5

Frequencies

GnomAD3 genomes AF: 0.00000930 AC: 1 AN: 107537 Hom.: 0 Cov.: 21

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: 0.0000192

Gnomad OTH AF: 0.00

GnomAD2 exomes AF: 0.00000565 AC: 1 AN: 177146 AF XY: 0.00

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000374

Gnomad ASJ exome AF: 0.00

Gnomad EAS 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: 0.0000183 AC: 20 AN: 1094136 Hom.: 0 Cov.: 30 AF XY: 0.0000139 AC XY: 5 AN XY: 360766

African (AFR) AF: 0.00 AC: 0 AN: 26307

American (AMR) AF: 0.0000285 AC: 1 AN: 35115

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 19313

East Asian (EAS) AF: 0.0000663 AC: 2 AN: 30178

South Asian (SAS) AF: 0.0000372 AC: 2 AN: 53833

European-Finnish (FIN) AF: 0.0000247 AC: 1 AN: 40503

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2882

European-Non Finnish (NFE) AF: 0.0000155 AC: 13 AN: 840142

Other (OTH) AF: 0.0000218 AC: 1 AN: 45863

GnomAD4 genome AF: 0.00000930 AC: 1 AN: 107537 Hom.: 0 Cov.: 21 AF XY: 0.0000334 AC XY: 1 AN XY: 29929

African (AFR) AF: 0.00 AC: 0 AN: 29519

American (AMR) AF: 0.00 AC: 0 AN: 9820

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2591

East Asian (EAS) AF: 0.00 AC: 0 AN: 3437

South Asian (SAS) AF: 0.00 AC: 0 AN: 2329

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5409

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 234

European-Non Finnish (NFE) AF: 0.0000192 AC: 1 AN: 52098

Other (OTH) AF: 0.00 AC: 0 AN: 1430

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.0000113

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.62
DANN	Benign	0.48
PhyloP100		-0.031

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

Other links and lift over

dbSNP: rs1342577940; hg19: chrX-52674544;