rs548622709
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002900.3(RBP3):c.2763C>A(p.Ser921Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000769 in 1,613,242 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 8/10 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002900.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBP3 | NM_002900.3 | c.2763C>A | p.Ser921Arg | missense_variant | 1/4 | ENST00000584701.2 | NP_002891.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBP3 | ENST00000584701.2 | c.2763C>A | p.Ser921Arg | missense_variant | 1/4 | 1 | NM_002900.3 | ENSP00000463151.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152244Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250956Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135804
GnomAD4 exome AF: 0.0000787 AC: 115AN: 1460998Hom.: 0 Cov.: 34 AF XY: 0.0000839 AC XY: 61AN XY: 726814
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152244Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74382
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jul 03, 2023 | 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. 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 disruptive. ClinVar contains an entry for this variant (Variation ID: 208321). This missense change has been observed in individual(s) with retinitis pigmentosa (PMID: 19074801). This variant is present in population databases (rs548622709, gnomAD 0.006%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 921 of the RBP3 protein (p.Ser921Arg). - |
Retinitis pigmentosa 66 Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | ClinVar Staff, National Center for Biotechnology Information (NCBI) | Jun 27, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at