rs370153105

Variant names:

• chr1-84656404-C-G
• rs370153105
• NM_001166293.2:c.1159G>C

Your query was ambiguous. Multiple possible variants found:

• chr1-84656404-C-G
• chr1-84656404-C-T

Variant summary

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

The NM_001166293.2(SSX2IP):​c.1159G>C​(p.Glu387Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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. E387K) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: SSX2IP NM_001166293.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.23

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 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=0.18262783).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SSX2IP	NM_001166293.2	c.1159G>C	p.Glu387Gln	missense_variant	Exon 10 of 14	ENST00000342203.8	NP_001159765.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SSX2IP	ENST00000342203.8	c.1159G>C	p.Glu387Gln	missense_variant	Exon 10 of 14	1	NM_001166293.2	ENSP00000340279.3
SSX2IP	ENST00000476905.6	n.1147G>C		non_coding_transcript_exon_variant	Exon 11 of 16	2		ENSP00000474925.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461090 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 726808

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

Asia WGS AF: 0.000867 AC: 3 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.083
BayesDel_addAF	Benign	-0.21	T
BayesDel_noAF	Benign	-0.53
CADD	Benign	20
DANN	Uncertain	0.98
DEOGEN2	Benign	0.054	.;T;.
Eigen	Benign	-0.15
Eigen_PC	Benign	-0.056
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Uncertain	0.89	D;D;.
M_CAP	Benign	0.0087	T
MetaRNN	Benign	0.18	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	0.92	.;L;.
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-0.92	N;N;.
REVEL	Benign	0.086
Sift	Benign	0.18	T;T;.
Sift4G	Benign	0.16	T;T;T
Polyphen		0.27	.;B;.
Vest4		0.25
MutPred		0.13		.;Loss of phosphorylation at T383 (P = 0.1797);.;
MVP		0.50
MPC		0.14
ClinPred		0.76	D
GERP RS		4.7
Varity_R		0.096
gMVP		0.22

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: rs370153105; hg19: chr1-85122087;