3-120694208-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PS1_ModerateBP4_ModerateBP6_ModerateBS2
The NM_173825.5(RABL3):c.551G>A(p.Arg184Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00146 in 1,610,670 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_173825.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RABL3 | NM_173825.5 | c.551G>A | p.Arg184Gln | missense_variant | 6/8 | ENST00000273375.8 | |
RABL3 | NM_001363965.1 | c.551G>A | p.Arg184Gln | missense_variant | 6/9 | ||
RABL3 | NM_001363964.1 | c.535-3721G>A | intron_variant | ||||
RABL3 | NR_157022.1 | n.865G>A | non_coding_transcript_exon_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RABL3 | ENST00000273375.8 | c.551G>A | p.Arg184Gln | missense_variant | 6/8 | 1 | NM_173825.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00103 AC: 156AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000677 AC: 170AN: 251104Hom.: 0 AF XY: 0.000678 AC XY: 92AN XY: 135730
GnomAD4 exome AF: 0.00150 AC: 2189AN: 1458502Hom.: 4 Cov.: 28 AF XY: 0.00145 AC XY: 1052AN XY: 725570
GnomAD4 genome ? AF: 0.00103 AC: 156AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.000860 AC XY: 64AN XY: 74384
ClinVar
Submissions by phenotype
RABL3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 12, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at