6-136792541-C-CCGCCG
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1BS2
The ENST00000698928.1(MAP3K5):c.96+103_96+104insCGGCG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0032 ( 2 hom., cov: 0)
Exomes 𝑓: 0.000062 ( 0 hom. )
Consequence
MAP3K5
ENST00000698928.1 intron
ENST00000698928.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.00
Genes affected
MAP3K5 (HGNC:6857): (mitogen-activated protein kinase kinase kinase 5) Mitogen-activated protein kinase (MAPK) signaling cascades include MAPK or extracellular signal-regulated kinase (ERK), MAPK kinase (MKK or MEK), and MAPK kinase kinase (MAPKKK or MEKK). MAPKK kinase/MEKK phosphorylates and activates its downstream protein kinase, MAPK kinase/MEK, which in turn activates MAPK. The kinases of these signaling cascades are highly conserved, and homologs exist in yeast, Drosophila, and mammalian cells. MAPKKK5 contains 1,374 amino acids with all 11 kinase subdomains. Northern blot analysis shows that MAPKKK5 transcript is abundantly expressed in human heart and pancreas. The MAPKKK5 protein phosphorylates and activates MKK4 (aliases SERK1, MAPKK4) in vitro, and activates c-Jun N-terminal kinase (JNK)/stress-activated protein kinase (SAPK) during transient expression in COS and 293 cells; MAPKKK5 does not activate MAPK/ERK. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00322 (480/149090) while in subpopulation EAS AF= 0.0193 (95/4910). AF 95% confidence interval is 0.0162. There are 2 homozygotes in gnomad4. There are 263 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
BS2
High AC in GnomAd4 at 480 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP3K5 | XM_011535839.4 | c.96+103_96+104insCGGCG | intron_variant | XP_011534141.2 | ||||
MAP3K5 | XM_017010872.2 | c.96+103_96+104insCGGCG | intron_variant | XP_016866361.1 | ||||
MAP3K5 | XM_017010873.2 | c.96+103_96+104insCGGCG | intron_variant | XP_016866362.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP3K5 | ENST00000698928.1 | c.96+103_96+104insCGGCG | intron_variant | ENSP00000514039 |
Frequencies
GnomAD3 genomes AF: 0.00320 AC: 477AN: 148980Hom.: 2 Cov.: 0
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GnomAD4 exome AF: 0.0000619 AC: 1AN: 16164Hom.: 0 Cov.: 0 AF XY: 0.000126 AC XY: 1AN XY: 7930
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GnomAD4 genome AF: 0.00322 AC: 480AN: 149090Hom.: 2 Cov.: 0 AF XY: 0.00362 AC XY: 263AN XY: 72712
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at