rs149207118
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_006267.5(RANBP2):c.1087C>T(p.Arg363Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00108 in 1,611,800 control chromosomes in the GnomAD database, including 18 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R363H) has been classified as Uncertain significance.
Frequency
Consequence
NM_006267.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP2 | NM_006267.5 | c.1087C>T | p.Arg363Cys | missense_variant | 9/29 | ENST00000283195.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP2 | ENST00000283195.11 | c.1087C>T | p.Arg363Cys | missense_variant | 9/29 | 1 | NM_006267.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00560 AC: 851AN: 152004Hom.: 9 Cov.: 31
GnomAD3 exomes AF: 0.00135 AC: 340AN: 250978Hom.: 4 AF XY: 0.000936 AC XY: 127AN XY: 135700
GnomAD4 exome AF: 0.000610 AC: 891AN: 1459678Hom.: 9 Cov.: 32 AF XY: 0.000518 AC XY: 376AN XY: 726144
GnomAD4 genome AF: 0.00559 AC: 851AN: 152122Hom.: 9 Cov.: 31 AF XY: 0.00553 AC XY: 411AN XY: 74354
ClinVar
Submissions by phenotype
Familial acute necrotizing encephalopathy Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Sep 13, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at