chr3-120698483-A-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_173825.5(RABL3):c.474T>C(p.His158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00825 in 1,614,008 control chromosomes in the GnomAD database, including 77 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0059 ( 2 hom., cov: 32)
Exomes 𝑓: 0.0085 ( 75 hom. )
Consequence
RABL3
NM_173825.5 synonymous
NM_173825.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.81
Genes affected
RABL3 (HGNC:18072): (RAB, member of RAS oncogene family like 3) Predicted to enable GTP binding activity; GTPase activity; and protein homodimerization activity. Involved in regulation of Ras protein signal transduction and regulation of protein lipidation. Predicted to be active in endomembrane system. Implicated in pancreatic cancer. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 3-120698483-A-G is Benign according to our data. Variant chr3-120698483-A-G is described in ClinVar as [Benign]. Clinvar id is 3037588.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=2.81 with no splicing effect.
BS2
?
High AC in GnomAd at 899 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RABL3 | NM_173825.5 | c.474T>C | p.His158= | synonymous_variant | 5/8 | ENST00000273375.8 | |
RABL3 | NM_001363965.1 | c.474T>C | p.His158= | synonymous_variant | 5/9 | ||
RABL3 | NM_001363964.1 | c.474T>C | p.His158= | synonymous_variant | 5/7 | ||
RABL3 | NR_157022.1 | n.788T>C | non_coding_transcript_exon_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RABL3 | ENST00000273375.8 | c.474T>C | p.His158= | synonymous_variant | 5/8 | 1 | NM_173825.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00591 AC: 899AN: 152210Hom.: 2 Cov.: 32
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GnomAD3 exomes AF: 0.00643 AC: 1617AN: 251344Hom.: 11 AF XY: 0.00635 AC XY: 863AN XY: 135840
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GnomAD4 exome AF: 0.00849 AC: 12415AN: 1461680Hom.: 75 Cov.: 30 AF XY: 0.00835 AC XY: 6073AN XY: 727152
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GnomAD4 genome ? AF: 0.00590 AC: 899AN: 152328Hom.: 2 Cov.: 32 AF XY: 0.00620 AC XY: 462AN XY: 74488
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
RABL3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 19, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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BayesDel_noAF
Benign
Cadd
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Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at