17-5335289-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_004703.6(RABEP1):āc.473G>Cā(p.Arg158Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,116 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 (ā ).
Frequency
Consequence
NM_004703.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RABEP1 | ENST00000537505.6 | c.473G>C | p.Arg158Thr | missense_variant | Exon 4 of 18 | 1 | NM_004703.6 | ENSP00000445408.2 | ||
RABEP1 | ENST00000341923.10 | c.473G>C | p.Arg158Thr | missense_variant | Exon 4 of 17 | 1 | ENSP00000339569.6 | |||
RABEP1 | ENST00000575475.2 | n.509G>C | non_coding_transcript_exon_variant | Exon 3 of 14 | 1 | |||||
RABEP1 | ENST00000570487.1 | c.203G>C | p.Arg68Thr | missense_variant | Exon 2 of 3 | 2 | ENSP00000482983.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249446Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135340
GnomAD4 exome Cov.: 30
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152116Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74290
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.473G>C (p.R158T) alteration is located in exon 4 (coding exon 4) of the RABEP1 gene. This alteration results from a G to C substitution at nucleotide position 473, causing the arginine (R) at amino acid position 158 to be replaced by a threonine (T). 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