rs141379413
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_006267.5(RANBP2):āc.5561A>Gā(p.Asn1854Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000278 in 1,614,158 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_006267.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP2 | NM_006267.5 | c.5561A>G | p.Asn1854Ser | missense_variant | 20/29 | ENST00000283195.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP2 | ENST00000283195.11 | c.5561A>G | p.Asn1854Ser | missense_variant | 20/29 | 1 | NM_006267.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000782 AC: 119AN: 152228Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000187 AC: 47AN: 250916Hom.: 0 AF XY: 0.000199 AC XY: 27AN XY: 135874
GnomAD4 exome AF: 0.000221 AC: 323AN: 1461812Hom.: 0 Cov.: 33 AF XY: 0.000199 AC XY: 145AN XY: 727214
GnomAD4 genome ? AF: 0.000827 AC: 126AN: 152346Hom.: 2 Cov.: 32 AF XY: 0.000966 AC XY: 72AN XY: 74498
ClinVar
Submissions by phenotype
Familial acute necrotizing encephalopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 13, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at