X-48187692-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_175723.2(SSX5):c.506G>A(p.Arg169His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000323 in 1,207,864 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 18 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 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 Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSX5 | NM_175723.2 | c.506G>A | p.Arg169His | missense_variant | Exon 7 of 8 | ENST00000347757.6 | NP_783729.1 | |
SSX5 | NM_021015.4 | c.629G>A | p.Arg210His | missense_variant | Exon 8 of 9 | NP_066295.3 | ||
SSX5 | XM_011543949.3 | c.506G>A | p.Arg169His | 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.506G>A | p.Arg169His | missense_variant | Exon 7 of 8 | 5 | NM_175723.2 | ENSP00000290558.1 | ||
SSX5 | ENST00000311798.5 | c.629G>A | p.Arg210His | missense_variant | Exon 8 of 9 | 5 | ENSP00000312415.1 | |||
SSX5 | ENST00000403001.3 | n.326G>A | non_coding_transcript_exon_variant | Exon 3 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000117 AC: 13AN: 111561Hom.: 0 Cov.: 23 AF XY: 0.000207 AC XY: 7AN XY: 33741
GnomAD3 exomes AF: 0.0000437 AC: 8AN: 183180Hom.: 0 AF XY: 0.0000590 AC XY: 4AN XY: 67764
GnomAD4 exome AF: 0.0000237 AC: 26AN: 1096253Hom.: 0 Cov.: 30 AF XY: 0.0000303 AC XY: 11AN XY: 362725
GnomAD4 genome AF: 0.000116 AC: 13AN: 111611Hom.: 0 Cov.: 23 AF XY: 0.000207 AC XY: 7AN XY: 33801
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.629G>A (p.R210H) alteration is located in exon 8 (coding exon 7) of the SSX5 gene. This alteration results from a G to A substitution at nucleotide position 629, causing the arginine (R) at amino acid position 210 to be replaced by a histidine (H). 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