2-108719689-C-G
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006267.5(RANBP2):c.72+11C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00875 in 1,597,440 control chromosomes in the GnomAD database, including 911 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006267.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RANBP2 | ENST00000283195.11 | c.72+11C>G | intron_variant | Intron 1 of 28 | 1 | NM_006267.5 | ENSP00000283195.6 | |||
RANBP2 | ENST00000697737.1 | c.72+11C>G | intron_variant | Intron 1 of 26 | ENSP00000513426.1 | |||||
RANBP2 | ENST00000425282.4 | n.72+11C>G | intron_variant | Intron 1 of 3 | 5 | ENSP00000398970.2 | ||||
RANBP2 | ENST00000697738.1 | n.181+11C>G | intron_variant | Intron 1 of 9 |
Frequencies
GnomAD3 genomes AF: 0.0429 AC: 6534AN: 152210Hom.: 480 Cov.: 32
GnomAD3 exomes AF: 0.0123 AC: 2718AN: 221162Hom.: 161 AF XY: 0.00941 AC XY: 1128AN XY: 119912
GnomAD4 exome AF: 0.00514 AC: 7421AN: 1445114Hom.: 429 Cov.: 30 AF XY: 0.00455 AC XY: 3264AN XY: 717536
GnomAD4 genome AF: 0.0430 AC: 6551AN: 152326Hom.: 482 Cov.: 32 AF XY: 0.0414 AC XY: 3084AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Familial acute necrotizing encephalopathy Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at