6-161034296-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005922.4(MAP3K4):c.190C>T(p.Pro64Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000563 in 1,613,788 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P64H) has been classified as Uncertain significance.
Frequency
Consequence
NM_005922.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00283 AC: 431AN: 152126Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000824 AC: 207AN: 251082Hom.: 2 AF XY: 0.000567 AC XY: 77AN XY: 135708
GnomAD4 exome AF: 0.000328 AC: 479AN: 1461544Hom.: 2 Cov.: 31 AF XY: 0.000267 AC XY: 194AN XY: 727076
GnomAD4 genome AF: 0.00282 AC: 430AN: 152244Hom.: 1 Cov.: 32 AF XY: 0.00262 AC XY: 195AN XY: 74440
ClinVar
Submissions by phenotype
not provided Benign:1
MAP3K4: BP4, BS1 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at