rs202005268
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_006267.5(RANBP2):c.6612C>A(p.Ala2204=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000775 in 1,611,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A2204A) has been classified as Benign.
Frequency
Consequence
NM_006267.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RANBP2 | NM_006267.5 | c.6612C>A | p.Ala2204= | synonymous_variant | 20/29 | ENST00000283195.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RANBP2 | ENST00000283195.11 | c.6612C>A | p.Ala2204= | synonymous_variant | 20/29 | 1 | NM_006267.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000572 AC: 87AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000643 AC: 159AN: 247326Hom.: 0 AF XY: 0.000625 AC XY: 84AN XY: 134476
GnomAD4 exome AF: 0.000796 AC: 1162AN: 1459702Hom.: 0 Cov.: 33 AF XY: 0.000756 AC XY: 549AN XY: 726156
GnomAD4 genome ? AF: 0.000572 AC: 87AN: 152118Hom.: 0 Cov.: 32 AF XY: 0.000498 AC XY: 37AN XY: 74306
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 28, 2017 | 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
Benign, criteria provided, single submitter | clinical testing | Invitae | Mar 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at