chr12-111892969-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_003668.4(MAPKAPK5):c.1324C>T(p.Arg442Cys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000639 in 1,565,820 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003668.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAPKAPK5 | NM_003668.4 | c.1324C>T | p.Arg442Cys | missense_variant, splice_region_variant | 14/14 | ENST00000550735.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAPKAPK5 | ENST00000550735.7 | c.1324C>T | p.Arg442Cys | missense_variant, splice_region_variant | 14/14 | 1 | NM_003668.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183016Hom.: 0 AF XY: 0.0000103 AC XY: 1AN XY: 97188
GnomAD4 exome AF: 0.00000637 AC: 9AN: 1413768Hom.: 0 Cov.: 29 AF XY: 0.00000715 AC XY: 5AN XY: 699014
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.1330C>T (p.R444C) alteration is located in exon 14 (coding exon 14) of the MAPKAPK5 gene. This alteration results from a C to T substitution at nucleotide position 1330, causing the arginine (R) at amino acid position 444 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at