X-48354677-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021014.4(SSX3):c.139G>A(p.Val47Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000746 in 1,206,031 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V47A) 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SSX3 | NM_021014.4 | c.139G>A | p.Val47Ile | missense_variant | Exon 3 of 8 | ENST00000298396.7 | NP_066294.1 | |
SSX3 | XM_011543885.3 | c.139G>A | p.Val47Ile | missense_variant | Exon 3 of 7 | XP_011542187.1 | ||
SSX3 | NR_176964.1 | n.229G>A | non_coding_transcript_exon_variant | Exon 3 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSX3 | ENST00000298396.7 | c.139G>A | p.Val47Ile | missense_variant | Exon 3 of 8 | 1 | NM_021014.4 | ENSP00000298396.2 | ||
SSX3 | ENST00000612497.1 | c.139G>A | p.Val47Ile | missense_variant | Exon 2 of 5 | 5 | ENSP00000480427.1 | |||
SSX3 | ENST00000376893.7 | c.139G>A | p.Val47Ile | missense_variant | Exon 3 of 8 | 2 | ENSP00000366090.3 |
Frequencies
GnomAD3 genomes AF: 0.0000273 AC: 3AN: 110069Hom.: 0 Cov.: 22 AF XY: 0.0000309 AC XY: 1AN XY: 32361
GnomAD3 exomes AF: 0.0000164 AC: 3AN: 182972Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67564
GnomAD4 exome AF: 0.00000547 AC: 6AN: 1095962Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 361664
GnomAD4 genome AF: 0.0000273 AC: 3AN: 110069Hom.: 0 Cov.: 22 AF XY: 0.0000309 AC XY: 1AN XY: 32361
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at