19-55489569-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001144950.2(SSC5D):c.268C>T(p.Arg90Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000113 in 1,510,894 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R90Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001144950.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SSC5D | ENST00000389623.11 | c.268C>T | p.Arg90Trp | missense_variant | Exon 3 of 14 | 1 | NM_001144950.2 | ENSP00000374274.4 | ||
SSC5D | ENST00000587166.5 | c.268C>T | p.Arg90Trp | missense_variant | Exon 3 of 13 | 1 | ENSP00000467252.1 | |||
SSC5D | ENST00000594321.5 | c.268C>T | p.Arg90Trp | missense_variant | Exon 3 of 3 | 4 | ENSP00000470226.1 | |||
SSC5D | ENST00000588254.1 | n.682C>T | non_coding_transcript_exon_variant | Exon 2 of 5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152146Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000110 AC: 15AN: 1358630Hom.: 0 Cov.: 33 AF XY: 0.0000105 AC XY: 7AN XY: 668758
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74462
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.268C>T (p.R90W) alteration is located in exon 3 (coding exon 3) of the SSC5D gene. This alteration results from a C to T substitution at nucleotide position 268, causing the arginine (R) at amino acid position 90 to be replaced by a tryptophan (W). 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