rs1799841
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001900.5(CST5):āc.136T>Cā(p.Cys46Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 1,613,572 control chromosomes in the GnomAD database, including 174,748 homozygotes. 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C46F) has been classified as Uncertain significance.
Frequency
Consequence
NM_001900.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CST5 | NM_001900.5 | c.136T>C | p.Cys46Arg | missense_variant | 1/3 | ENST00000304710.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CST5 | ENST00000304710.5 | c.136T>C | p.Cys46Arg | missense_variant | 1/3 | 1 | NM_001900.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.535 AC: 81230AN: 151762Hom.: 23230 Cov.: 32
GnomAD3 exomes AF: 0.482 AC: 121082AN: 251316Hom.: 30495 AF XY: 0.470 AC XY: 63782AN XY: 135816
GnomAD4 exome AF: 0.451 AC: 659059AN: 1461694Hom.: 151476 Cov.: 51 AF XY: 0.450 AC XY: 326915AN XY: 727162
GnomAD4 genome AF: 0.535 AC: 81326AN: 151878Hom.: 23272 Cov.: 32 AF XY: 0.537 AC XY: 39829AN XY: 74204
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at