rs200400906
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PP3_ModerateBS2
The NM_001011.4(RPS7):c.433C>T(p.Arg145Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000089 in 1,461,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 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. R145H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001011.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RPS7 | NM_001011.4 | c.433C>T | p.Arg145Cys | missense_variant | 6/7 | ENST00000645674.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RPS7 | ENST00000645674.2 | c.433C>T | p.Arg145Cys | missense_variant | 6/7 | NM_001011.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 0AN: 151630Hom.: 0 Cov.: 32 FAILED QC
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251276Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135796
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461412Hom.: 0 Cov.: 32 AF XY: 0.00000825 AC XY: 6AN XY: 727036
GnomAD4 genome ? Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 151630Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74010
ClinVar
Submissions by phenotype
Diamond-Blackfan anemia 8 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Sep 05, 2023 | An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 145 of the RPS7 protein (p.Arg145Cys). This variant is present in population databases (rs200400906, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with RPS7-related conditions. ClinVar contains an entry for this variant (Variation ID: 577746). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at