X-48194150-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.259G>A(p.Asp87Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000621 in 1,207,907 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 20 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.259G>A | p.Asp87Asn | missense_variant | Exon 4 of 8 | ENST00000347757.6 | NP_783729.1 | |
SSX5 | NM_021015.4 | c.382G>A | p.Asp128Asn | missense_variant | Exon 5 of 9 | NP_066295.3 | ||
SSX5 | XM_011543949.3 | c.259G>A | p.Asp87Asn | missense_variant | Exon 4 of 8 | XP_011542251.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000454 AC: 5AN: 110164Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32408
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183347Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67857
GnomAD4 exome AF: 0.0000638 AC: 70AN: 1097743Hom.: 0 Cov.: 31 AF XY: 0.0000551 AC XY: 20AN XY: 363211
GnomAD4 genome AF: 0.0000454 AC: 5AN: 110164Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32408
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.382G>A (p.D128N) alteration is located in exon 5 (coding exon 4) of the SSX5 gene. This alteration results from a G to A substitution at nucleotide position 382, causing the aspartic acid (D) at amino acid position 128 to be replaced by an asparagine (N). 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