10-93593818-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The ENST00000371464.8(RBP4):c.568+5G>T variant causes a splice donor 5th base, intron change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000371464.8 splice_donor_5th_base, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBP4 | NM_006744.4 | c.568+5G>T | splice_donor_5th_base_variant, intron_variant | ENST00000371464.8 | NP_006735.2 | |||
RBP4 | NM_001323517.1 | c.568+5G>T | splice_donor_5th_base_variant, intron_variant | NP_001310446.1 | ||||
RBP4 | NM_001323518.2 | c.562+5G>T | splice_donor_5th_base_variant, intron_variant | NP_001310447.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBP4 | ENST00000371464.8 | c.568+5G>T | splice_donor_5th_base_variant, intron_variant | 1 | NM_006744.4 | ENSP00000360519 | P1 | |||
RBP4 | ENST00000371467.5 | c.568+5G>T | splice_donor_5th_base_variant, intron_variant | 5 | ENSP00000360522 | P1 | ||||
RBP4 | ENST00000371469.2 | c.562+5G>T | splice_donor_5th_base_variant, intron_variant | 5 | ENSP00000360524 | |||||
FFAR4 | ENST00000604414.1 | c.697-10256C>A | intron_variant | 3 | ENSP00000474477 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 10, 2020 | This sequence change falls in intron 5 of the RBP4 gene. It does not directly change the encoded amino acid sequence of the RBP4 protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with RBP4-related conditions. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. 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
Publications
No publications associated with this variant yet.