X-48187636-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_175723.2(SSX5):c.562G>C(p.Glu188Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000663 in 1,207,119 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 27 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_175723.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSX5 | NM_175723.2 | c.562G>C | p.Glu188Gln | missense_variant | Exon 7 of 8 | ENST00000347757.6 | NP_783729.1 | |
SSX5 | NM_021015.4 | c.685G>C | p.Glu229Gln | missense_variant | Exon 8 of 9 | NP_066295.3 | ||
SSX5 | XM_011543949.3 | c.562G>C | p.Glu188Gln | missense_variant | Exon 7 of 8 | XP_011542251.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSX5 | ENST00000347757.6 | c.562G>C | p.Glu188Gln | missense_variant | Exon 7 of 8 | 5 | NM_175723.2 | ENSP00000290558.1 | ||
SSX5 | ENST00000311798.5 | c.685G>C | p.Glu229Gln | missense_variant | Exon 8 of 9 | 5 | ENSP00000312415.1 | |||
SSX5 | ENST00000403001.3 | n.382G>C | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000358 AC: 4AN: 111746Hom.: 0 Cov.: 23 AF XY: 0.0000589 AC XY: 2AN XY: 33952
GnomAD3 exomes AF: 0.0000929 AC: 17AN: 182957Hom.: 0 AF XY: 0.000133 AC XY: 9AN XY: 67547
GnomAD4 exome AF: 0.0000694 AC: 76AN: 1095373Hom.: 0 Cov.: 30 AF XY: 0.0000691 AC XY: 25AN XY: 361911
GnomAD4 genome AF: 0.0000358 AC: 4AN: 111746Hom.: 0 Cov.: 23 AF XY: 0.0000589 AC XY: 2AN XY: 33952
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.685G>C (p.E229Q) alteration is located in exon 8 (coding exon 7) of the SSX5 gene. This alteration results from a G to C substitution at nucleotide position 685, causing the glutamic acid (E) at amino acid position 229 to be replaced by a glutamine (Q). 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