rs10493751

Variant names:

• chr1-84655414-A-C
• rs10493751
• NM_001166293.2:c.1389+418T>G

Your query was ambiguous. Multiple possible variants found:

• chr1-84655414-A-C
• chr1-84655414-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001166293.2(SSX2IP):​c.1389+418T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000088 in 1,136,074 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 8.8e-7 (0 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

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSX2IP	NM_001166293.2	c.1389+418T>G		intron_variant	Intron 11 of 13	ENST00000342203.8	NP_001159765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSX2IP	ENST00000342203.8	c.1389+418T>G		intron_variant	Intron 11 of 13	1	NM_001166293.2	ENSP00000340279.3
SSX2IP	ENST00000476905.6	n.1501+51T>G		intron_variant	Intron 13 of 15	2		ENSP00000474925.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 8.80e-7 AC: 1 AN: 1136074 Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0 AN XY: 557170

Gnomad4 AFR exome AF: 0.00 AC: 0 AN: 24344

Gnomad4 AMR exome AF: 0.00 AC: 0 AN: 28072

Gnomad4 ASJ exome AF: 0.00 AC: 0 AN: 15888

Gnomad4 EAS exome AF: 0.00 AC: 0 AN: 12840

Gnomad4 SAS exome AF: 0.00 AC: 0 AN: 75620

Gnomad4 FIN exome AF: 0.00 AC: 0 AN: 12716

Gnomad4 NFE exome AF: 0.00000109 AC: 1 AN: 920778

Gnomad4 Remaining exome AF: 0.00 AC: 0 AN: 41462

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.017
DANN	Benign	0.65

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;