3-120730727-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM4
The NM_173825.5(RABL3):c.107C>A(p.Ser36Ter) variant causes a stop gained change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000483 in 1,613,752 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 risk factor (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_173825.5 stop_gained
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 |
---|---|---|---|---|---|---|---|
RABL3 | NM_173825.5 | c.107C>A | p.Ser36Ter | stop_gained | 2/8 | ENST00000273375.8 | |
RABL3 | NM_001363965.1 | c.107C>A | p.Ser36Ter | stop_gained | 2/9 | ||
RABL3 | NM_001363964.1 | c.107C>A | p.Ser36Ter | stop_gained | 2/7 | ||
RABL3 | NR_157022.1 | n.421C>A | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RABL3 | ENST00000273375.8 | c.107C>A | p.Ser36Ter | stop_gained | 2/8 | 1 | NM_173825.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251356Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135832
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461596Hom.: 0 Cov.: 29 AF XY: 0.0000509 AC XY: 37AN XY: 727100
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152156Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74330
ClinVar
Submissions by phenotype
Pancreatic cancer, susceptibility to, 5 Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Nov 26, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at