X-48350117-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_021014.4(SSX3):c.336G>A(p.Met112Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000024 in 1,209,751 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 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 (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.
Frequency
Consequence
NM_021014.4 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 |
---|---|---|---|---|---|---|---|---|
SSX3 | NM_021014.4 | c.336G>A | p.Met112Ile | missense_variant | Exon 6 of 8 | ENST00000298396.7 | NP_066294.1 | |
SSX3 | XM_011543885.3 | c.336G>A | p.Met112Ile | missense_variant | Exon 6 of 7 | XP_011542187.1 | ||
SSX3 | NR_176964.1 | n.426G>A | 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.336G>A | p.Met112Ile | missense_variant | Exon 6 of 8 | 1 | NM_021014.4 | ENSP00000298396.2 | ||
SSX3 | ENST00000612497.1 | c.336G>A | p.Met112Ile | missense_variant | Exon 5 of 5 | 5 | ENSP00000480427.1 | |||
SSX3 | ENST00000376893.7 | c.336G>A | p.Met112Ile | missense_variant | Exon 6 of 8 | 2 | ENSP00000366090.3 | |||
SSX3 | ENST00000376895.2 | n.154G>A | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111721Hom.: 0 Cov.: 22 AF XY: 0.0000295 AC XY: 1AN XY: 33897
GnomAD3 exomes AF: 0.0000273 AC: 5AN: 183309Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67749
GnomAD4 exome AF: 0.0000246 AC: 27AN: 1098030Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 8AN XY: 363394
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111721Hom.: 0 Cov.: 22 AF XY: 0.0000295 AC XY: 1AN XY: 33897
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.336G>A (p.M112I) alteration is located in exon 6 (coding exon 5) of the SSX3 gene. This alteration results from a G to A substitution at nucleotide position 336, causing the methionine (M) at amino acid position 112 to be replaced by an isoleucine (I). 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