NM_005492.4:c.279C>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005492.4(CST8):c.279C>A(p.Ser93Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000203 in 1,613,060 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005492.4 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 |
---|---|---|---|---|---|---|---|---|
CST8 | NM_005492.4 | c.279C>A | p.Ser93Arg | missense_variant | Exon 3 of 4 | ENST00000246012.2 | NP_005483.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CST8 | ENST00000246012.2 | c.279C>A | p.Ser93Arg | missense_variant | Exon 3 of 4 | 1 | NM_005492.4 | ENSP00000246012.1 | ||
CST8 | ENST00000449810.5 | c.279C>A | p.Ser93Arg | missense_variant | Exon 3 of 4 | 3 | ENSP00000399144.1 | |||
ENSG00000260202 | ENST00000619495.1 | n.439-11242G>T | intron_variant | Intron 1 of 1 | 4 |
Frequencies
GnomAD3 genomes AF: 0.000645 AC: 98AN: 151990Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000366 AC: 92AN: 251408Hom.: 0 AF XY: 0.000294 AC XY: 40AN XY: 135880
GnomAD4 exome AF: 0.000157 AC: 230AN: 1460954Hom.: 0 Cov.: 30 AF XY: 0.000144 AC XY: 105AN XY: 726866
GnomAD4 genome AF: 0.000644 AC: 98AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.000605 AC XY: 45AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.279C>A (p.S93R) alteration is located in exon 3 (coding exon 2) of the CST8 gene. This alteration results from a C to A substitution at nucleotide position 279, causing the serine (S) at amino acid position 93 to be replaced by an arginine (R). 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