chr11-110233414-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_002906.4(RDX):c.1410C>A(p.Pro470=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000287 in 1,614,026 control chromosomes in the GnomAD database, including 5 homozygotes. 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. P470P) has been classified as Likely benign.
Frequency
Consequence
NM_002906.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDX | NM_002906.4 | c.1410C>A | p.Pro470= | synonymous_variant | 13/14 | ENST00000645495.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDX | ENST00000645495.2 | c.1410C>A | p.Pro470= | synonymous_variant | 13/14 | NM_002906.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 152080Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000521 AC: 131AN: 251396Hom.: 0 AF XY: 0.000640 AC XY: 87AN XY: 135868
GnomAD4 exome AF: 0.000293 AC: 429AN: 1461828Hom.: 4 Cov.: 33 AF XY: 0.000367 AC XY: 267AN XY: 727210
GnomAD4 genome AF: 0.000230 AC: 35AN: 152198Hom.: 1 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 03, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 18, 2023 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 06, 2013 | p.Pro470Pro in exon 13 of RDX: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue and is not found withi n the splice consensus sequence. This variant has been identified in 0.4% (118/3 0780) of South Asian chromosomes by the Genome Aggregation Database (gnomAD, htt p://gnomAD.broadinstitute.org; dbSNP rs577555846). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at