1-46580565-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001135553.4(MKNK1):c.163G>A(p.Val55Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001135553.4 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MKNK1 | NM_001135553.4 | c.163G>A | p.Val55Met | missense_variant | 4/13 | ENST00000371945.10 | NP_001129025.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MKNK1 | ENST00000371945.10 | c.163G>A | p.Val55Met | missense_variant | 4/13 | 1 | NM_001135553.4 | ENSP00000361013.5 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152208Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251406Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135874
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461724Hom.: 0 Cov.: 30 AF XY: 0.0000275 AC XY: 20AN XY: 727172
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | The c.199G>A (p.V67M) alteration is located in exon 4 (coding exon 3) of the MKNK1 gene. This alteration results from a G to A substitution at nucleotide position 199, causing the valine (V) at amino acid position 67 to be replaced by a methionine (M). 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