rs826549
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_006267.5(RANBP2):c.2550A>G(p.Ser850Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 150,522 control chromosomes in the GnomAD database, including 12,730 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006267.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RANBP2 | ENST00000283195.11 | c.2550A>G | p.Ser850Ser | synonymous_variant | Exon 18 of 29 | 1 | NM_006267.5 | ENSP00000283195.6 | ||
RANBP2 | ENST00000697737.1 | c.2550A>G | p.Ser850Ser | synonymous_variant | Exon 18 of 27 | ENSP00000513426.1 | ||||
RANBP2 | ENST00000697740.1 | c.2472A>G | p.Ser824Ser | synonymous_variant | Exon 18 of 27 | ENSP00000513427.1 |
Frequencies
GnomAD3 genomes AF: 0.353 AC: 53075AN: 150404Hom.: 12680 Cov.: 27
GnomAD3 exomes AF: 0.246 AC: 61490AN: 249652Hom.: 10250 AF XY: 0.246 AC XY: 33289AN XY: 135134
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.248 AC: 360529AN: 1456270Hom.: 49902 Cov.: 40 AF XY: 0.249 AC XY: 180793AN XY: 724664
GnomAD4 genome AF: 0.353 AC: 53188AN: 150522Hom.: 12730 Cov.: 27 AF XY: 0.347 AC XY: 25551AN XY: 73562
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