12-111893050-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003668.4(MAPKAPK5):c.1405G>A(p.Glu469Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000153 in 1,573,306 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. E469D) has been classified as Uncertain significance.
Frequency
Consequence
NM_003668.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPKAPK5 | NM_003668.4 | c.1405G>A | p.Glu469Lys | missense_variant | 14/14 | ENST00000550735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPKAPK5 | ENST00000550735.7 | c.1405G>A | p.Glu469Lys | missense_variant | 14/14 | 1 | NM_003668.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152126Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000120 AC: 17AN: 1421180Hom.: 0 Cov.: 29 AF XY: 0.0000114 AC XY: 8AN XY: 703344
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74324
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 26, 2022 | In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at