X-52645523-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_173358.2(SSX7):c.487G>A(p.Ala163Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,198,558 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173358.2 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 |
---|---|---|---|---|---|---|---|---|
SSX7 | NM_173358.2 | c.487G>A | p.Ala163Thr | missense_variant | Exon 7 of 8 | ENST00000298181.6 | NP_775494.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000467 AC: 5AN: 107035Hom.: 0 Cov.: 20 AF XY: 0.0000339 AC XY: 1AN XY: 29467
GnomAD3 exomes AF: 0.0000172 AC: 3AN: 174063Hom.: 0 AF XY: 0.0000164 AC XY: 1AN XY: 60855
GnomAD4 exome AF: 0.0000431 AC: 47AN: 1091523Hom.: 0 Cov.: 30 AF XY: 0.0000418 AC XY: 15AN XY: 358589
GnomAD4 genome AF: 0.0000467 AC: 5AN: 107035Hom.: 0 Cov.: 20 AF XY: 0.0000339 AC XY: 1AN XY: 29467
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.487G>A (p.A163T) alteration is located in exon 7 (coding exon 6) of the SSX7 gene. This alteration results from a G to A substitution at nucleotide position 487, causing the alanine (A) at amino acid position 163 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