2-108719608-T-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PVS1_SupportingPM2
The NM_006267.5(RANBP2):c.2T>A(p.Met1?) variant causes a start lost change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006267.5 start_lost
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RANBP2 | ENST00000283195.11 | c.2T>A | p.Met1? | start_lost | Exon 1 of 29 | 1 | NM_006267.5 | ENSP00000283195.6 | ||
RANBP2 | ENST00000697737.1 | c.2T>A | p.Met1? | start_lost | Exon 1 of 27 | ENSP00000513426.1 | ||||
RANBP2 | ENST00000425282.4 | n.2T>A | non_coding_transcript_exon_variant | Exon 1 of 4 | 5 | ENSP00000398970.2 | ||||
RANBP2 | ENST00000697738.1 | n.111T>A | non_coding_transcript_exon_variant | Exon 1 of 10 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Familial acute necrotizing encephalopathy Uncertain:1
Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. ClinVar contains an entry for this variant (Variation ID: 1025191). This variant has not been reported in the literature in individuals affected with RANBP2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change affects the initiator methionine of the RANBP2 mRNA. The next in-frame methionine is located at codon 27. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at