chr1-84656404-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001166293.2(SSX2IP):c.1159G>A(p.Glu387Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0000322 in 1,613,232 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001166293.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSX2IP | ENST00000342203.8 | c.1159G>A | p.Glu387Lys | missense_variant | Exon 10 of 14 | 1 | NM_001166293.2 | ENSP00000340279.3 | ||
SSX2IP | ENST00000476905.6 | n.1147G>A | non_coding_transcript_exon_variant | Exon 11 of 16 | 2 | ENSP00000474925.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250836Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135594
GnomAD4 exome AF: 0.0000329 AC: 48AN: 1461090Hom.: 0 Cov.: 31 AF XY: 0.0000344 AC XY: 25AN XY: 726808
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1159G>A (p.E387K) alteration is located in exon 11 (coding exon 9) of the SSX2IP gene. This alteration results from a G to A substitution at nucleotide position 1159, causing the glutamic acid (E) at amino acid position 387 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at