5-56816031-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM5BP4_ModerateBS2
The NM_005921.2(MAP3K1):āc.458C>Gā(p.Pro153Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000491 in 1,221,936 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P153L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_005921.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000659 AC: 1AN: 151732Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000467 AC: 5AN: 1070204Hom.: 0 Cov.: 38 AF XY: 0.00000197 AC XY: 1AN XY: 507426
GnomAD4 genome AF: 0.00000659 AC: 1AN: 151732Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74110
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at