chr17-5338079-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004703.6(RABEP1):c.589G>A(p.Ala197Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,228 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RABEP1 | NM_004703.6 | c.589G>A | p.Ala197Thr | missense_variant | 5/18 | ENST00000537505.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RABEP1 | ENST00000537505.6 | c.589G>A | p.Ala197Thr | missense_variant | 5/18 | 1 | NM_004703.6 | P1 | |
RABEP1 | ENST00000341923.10 | c.589G>A | p.Ala197Thr | missense_variant | 5/17 | 1 | |||
RABEP1 | ENST00000575475.2 | n.625G>A | non_coding_transcript_exon_variant | 4/14 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249364Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135290
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461228Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726926
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.589G>A (p.A197T) alteration is located in exon 5 (coding exon 5) of the RABEP1 gene. This alteration results from a G to A substitution at nucleotide position 589, causing the alanine (A) at amino acid position 197 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