chr11-75404831-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_001005.5(RPS3):c.698C>T(p.Pro233Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,612,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001005.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS3 | NM_001005.5 | c.698C>T | p.Pro233Leu | missense_variant | 6/7 | ENST00000531188.6 | |
RPS3 | NM_001260506.2 | c.746C>T | p.Pro249Leu | missense_variant | 6/7 | ||
RPS3 | NM_001256802.2 | c.698C>T | p.Pro233Leu | missense_variant | 6/7 | ||
RPS3 | NM_001260507.2 | c.320C>T | p.Pro107Leu | missense_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS3 | ENST00000531188.6 | c.698C>T | p.Pro233Leu | missense_variant | 6/7 | 1 | NM_001005.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000789 AC: 12AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000101 AC: 25AN: 247388Hom.: 0 AF XY: 0.000127 AC XY: 17AN XY: 134358
GnomAD4 exome AF: 0.0000479 AC: 70AN: 1460542Hom.: 0 Cov.: 31 AF XY: 0.0000482 AC XY: 35AN XY: 726464
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74474
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2023 | The c.698C>T (p.P233L) alteration is located in exon 6 (coding exon 6) of the RPS3 gene. This alteration results from a C to T substitution at nucleotide position 698, causing the proline (P) at amino acid position 233 to be replaced by a leucine (L). 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