17-5335301-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004703.6(RABEP1):c.485C>A(p.Ser162Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,268 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. S162C) has been classified as Uncertain significance.
Frequency
Consequence
NM_004703.6 missense
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 | UniProt |
---|---|---|---|---|---|---|---|
RABEP1 | NM_004703.6 | c.485C>A | p.Ser162Tyr | missense_variant | 4/18 | ENST00000537505.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RABEP1 | ENST00000537505.6 | c.485C>A | p.Ser162Tyr | missense_variant | 4/18 | 1 | NM_004703.6 | P1 | |
RABEP1 | ENST00000341923.10 | c.485C>A | p.Ser162Tyr | missense_variant | 4/17 | 1 | |||
RABEP1 | ENST00000575475.2 | n.521C>A | non_coding_transcript_exon_variant | 3/14 | 1 | ||||
RABEP1 | ENST00000570487.1 | c.218C>A | p.Ser73Tyr | missense_variant | 2/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151702Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249400Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135314
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461566Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727118
GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151702Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74058
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2023 | The c.485C>A (p.S162Y) alteration is located in exon 4 (coding exon 4) of the RABEP1 gene. This alteration results from a C to A substitution at nucleotide position 485, causing the serine (S) at amino acid position 162 to be replaced by a tyrosine (Y). 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