rs10493751

chr1-84655414-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_001166293.2(SSX2IP):c.1389+418T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0193 in 1,288,222 control chromosomes in the GnomAD database, including 293 homozygotes. 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 0.017 (32 hom., cov: 31)
  • Exomes 𝑓: 0.020 (261 hom.)
• Consequence: SSX2IP NM_001166293.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

Genes affected

SSX2IP (HGNC:16509): (SSX family member 2 interacting protein) This gene encodes a protein that binds the cancer-testis antigen Synovial Sarcoma X breakpoint 2 protein. The encoded protein may regulate the activity of Synovial Sarcoma X breakpoint 2 protein in malignant cells. Alternate splicing results in multiple transcript variants. A pseudogene of this gene is found on chromosome 3. [provided by RefSeq, Oct 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.017 (2588/152182) while in subpopulation NFE AF= 0.022 (1497/67976). AF 95% confidence interval is 0.0211. There are 32 homozygotes in gnomad4. There are 1341 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 32 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SSX2IP	NM_001166293.2	c.1389+418T>C		intron_variant		ENST00000342203.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SSX2IP	ENST00000342203.8	c.1389+418T>C		intron_variant		1	NM_001166293.2	P1

Frequencies

GnomAD3 genomes AF: 0.0170 AC: 2589 AN: 152064 Hom.: 32 Cov.: 31

Gnomad AFR AF: 0.00316

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.0163

Gnomad ASJ AF: 0.0216

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00829

Gnomad FIN AF: 0.0509

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0201

GnomAD4 exome AF: 0.0196 AC: 22284 AN: 1136040 Hom.: 261 Cov.: 32 AF XY: 0.0192 AC XY: 10725 AN XY: 557154

Gnomad4 AFR exome AF: 0.00353

Gnomad4 AMR exome AF: 0.0108

Gnomad4 ASJ exome AF: 0.0196

Gnomad4 EAS exome AF: 0.000156

Gnomad4 SAS exome AF: 0.00713

Gnomad4 FIN exome AF: 0.0524

Gnomad4 NFE exome AF: 0.0211

Gnomad4 OTH exome AF: 0.0183

GnomAD4 genome AF: 0.0170 AC: 2588 AN: 152182 Hom.: 32 Cov.: 31 AF XY: 0.0180 AC XY: 1341 AN XY: 74398

Gnomad4 AFR AF: 0.00315

Gnomad4 AMR AF: 0.0163

Gnomad4 ASJ AF: 0.0216

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00830

Gnomad4 FIN AF: 0.0509

Gnomad4 NFE AF: 0.0220

Gnomad4 OTH AF: 0.0199

Alfa AF: 0.0188 Hom.: 8

Bravo AF: 0.0141

Asia WGS AF: 0.00404 AC: 14 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	0.055
Dann	Benign	0.67

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

Other links and lift over

dbSNP: rs10493751; hg19: chr1-85121097;