rs727503393
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_002906.4(RDX):c.1341C>A(p.His447Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,452,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002906.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RDX | NM_002906.4 | c.1341C>A | p.His447Gln | missense_variant | 12/14 | ENST00000645495.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RDX | ENST00000645495.2 | c.1341C>A | p.His447Gln | missense_variant | 12/14 | NM_002906.4 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1452848Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 723358
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 17, 2014 | His447Gln in exon 12 of RDX: This variant is not expected to have clinical signi ficance due to a lack of conservation across species, including mammals. Of note , several bat species as well as other distant species have a glutamine (Gln) at this position, suggesting that this change can be tolerated. In addition, compu tational prediction tools suggest that the His447Gln variant may not impact the protein. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at