6-136567725-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005923.4(MAP3K5):c.3667G>A(p.Val1223Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000421 in 1,613,936 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005923.4 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
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP3K5 | ENST00000359015.5 | c.3667G>A | p.Val1223Met | missense_variant | Exon 26 of 30 | 1 | NM_005923.4 | ENSP00000351908.4 | ||
MAP3K5 | ENST00000698928.1 | c.3994G>A | p.Val1332Met | missense_variant | Exon 27 of 31 | ENSP00000514039.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251092Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135704
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461760Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727164
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3667G>A (p.V1223M) alteration is located in exon 26 (coding exon 26) of the MAP3K5 gene. This alteration results from a G to A substitution at nucleotide position 3667, causing the valine (V) at amino acid position 1223 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