X-48350080-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021014.4(SSX3):āc.373G>Cā(p.Glu125Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000894 in 111,916 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E125K) has been classified as Uncertain significance.
Frequency
Consequence
NM_021014.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSX3 | NM_021014.4 | c.373G>C | p.Glu125Gln | missense_variant | Exon 6 of 8 | ENST00000298396.7 | NP_066294.1 | |
SSX3 | XM_011543885.3 | c.373G>C | p.Glu125Gln | missense_variant | Exon 6 of 7 | XP_011542187.1 | ||
SSX3 | NR_176964.1 | n.463G>C | non_coding_transcript_exon_variant | Exon 6 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSX3 | ENST00000298396.7 | c.373G>C | p.Glu125Gln | missense_variant | Exon 6 of 8 | 1 | NM_021014.4 | ENSP00000298396.2 | ||
SSX3 | ENST00000612497.1 | c.373G>C | p.Glu125Gln | missense_variant | Exon 5 of 5 | 5 | ENSP00000480427.1 | |||
SSX3 | ENST00000376893.7 | c.373G>C | p.Glu125Gln | missense_variant | Exon 6 of 8 | 2 | ENSP00000366090.3 | |||
SSX3 | ENST00000376895.2 | n.191G>C | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000894 AC: 1AN: 111916Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34082
GnomAD4 exome Cov.: 32
GnomAD4 genome AF: 0.00000894 AC: 1AN: 111916Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34082
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at