6-136580331-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_005923.4(MAP3K5):c.3487G>A(p.Val1163Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,272 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. V1163L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005923.4 missense
Scores
Clinical Significance
Conservation
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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.3487G>A | p.Val1163Ile | missense_variant | Exon 25 of 30 | 1 | NM_005923.4 | ENSP00000351908.4 | ||
MAP3K5 | ENST00000698928.1 | c.3814G>A | p.Val1272Ile | missense_variant | Exon 26 of 31 | ENSP00000514039.1 | ||||
MAP3K5 | ENST00000463140.1 | n.*3G>A | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251430Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135888
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1461102Hom.: 0 Cov.: 29 AF XY: 0.00000688 AC XY: 5AN XY: 726836
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74330
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at