X-48354086-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021014.4(SSX3):c.193G>A(p.Ala65Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021014.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSX3 | NM_021014.4 | c.193G>A | p.Ala65Thr | missense_variant | Exon 4 of 8 | ENST00000298396.7 | NP_066294.1 | |
SSX3 | XM_011543885.3 | c.193G>A | p.Ala65Thr | missense_variant | Exon 4 of 7 | XP_011542187.1 | ||
SSX3 | NR_176964.1 | n.283G>A | non_coding_transcript_exon_variant | Exon 4 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSX3 | ENST00000298396.7 | c.193G>A | p.Ala65Thr | missense_variant | Exon 4 of 8 | 1 | NM_021014.4 | ENSP00000298396.2 | ||
SSX3 | ENST00000612497.1 | c.193G>A | p.Ala65Thr | missense_variant | Exon 3 of 5 | 5 | ENSP00000480427.1 | |||
SSX3 | ENST00000376893.7 | c.193G>A | p.Ala65Thr | missense_variant | Exon 4 of 8 | 2 | ENSP00000366090.3 |
Frequencies
GnomAD3 genomes Cov.: 21
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 21
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.193G>A (p.A65T) alteration is located in exon 4 (coding exon 3) of the SSX3 gene. This alteration results from a G to A substitution at nucleotide position 193, causing the alanine (A) at amino acid position 65 to be replaced by a threonine (T). 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
Publications
No publications associated with this variant yet.