16-2263161-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_080594.4(RNPS1):āc.354C>Gā(p.Ser118Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00000868 in 1,613,762 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S118N) has been classified as Uncertain significance.
Frequency
Consequence
NM_080594.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNPS1 | NM_080594.4 | c.354C>G | p.Ser118Arg | missense_variant | 4/8 | ENST00000320225.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNPS1 | ENST00000320225.10 | c.354C>G | p.Ser118Arg | missense_variant | 4/8 | 1 | NM_080594.4 | A1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000806 AC: 2AN: 248278Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134604
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461554Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727050
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.354C>G (p.S118R) alteration is located in exon 4 (coding exon 3) of the RNPS1 gene. This alteration results from a C to G substitution at nucleotide position 354, causing the serine (S) at amino acid position 118 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