1-84655953-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001166293.2(SSX2IP):c.1268G>A(p.Cys423Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,448 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSX2IP | ENST00000342203.8 | c.1268G>A | p.Cys423Tyr | missense_variant | Exon 11 of 14 | 1 | NM_001166293.2 | ENSP00000340279.3 | ||
SSX2IP | ENST00000476905.6 | n.1256G>A | non_coding_transcript_exon_variant | Exon 12 of 16 | 2 | ENSP00000474925.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250752Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135598
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461448Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727064
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1268G>A (p.C423Y) alteration is located in exon 12 (coding exon 10) of the SSX2IP gene. This alteration results from a G to A substitution at nucleotide position 1268, causing the cysteine (C) at amino acid position 423 to be replaced by a tyrosine (Y). 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