chr17-12141985-T-TG
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Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_003010.4(MAP2K4):c.*728dup variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0208 in 233,360 control chromosomes in the GnomAD database, including 59 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.021 ( 36 hom., cov: 32)
Exomes 𝑓: 0.021 ( 23 hom. )
Consequence
MAP2K4
NM_003010.4 3_prime_UTR
NM_003010.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.54
Genes affected
MAP2K4 (HGNC:6844): (mitogen-activated protein kinase kinase 4) This gene encodes a member of the mitogen-activated protein kinase (MAPK) family. Members of this family act as an integration point for multiple biochemical signals and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation, and development. They form a three-tiered signaling module composed of MAPKKKs, MAPKKs, and MAPKs. This protein is phosphorylated at serine and threonine residues by MAPKKKs and subsequently phosphorylates downstream MAPK targets at threonine and tyrosine residues. A similar protein in mouse has been reported to play a role in liver organogenesis. A pseudogene of this gene is located on the long arm of chromosome X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0541 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP2K4 | NM_003010.4 | c.*728dup | 3_prime_UTR_variant | 11/11 | ENST00000353533.10 | ||
MAP2K4 | NM_001281435.2 | c.*728dup | 3_prime_UTR_variant | 12/12 | |||
MAP2K4 | XM_005256753.4 | c.*728dup | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP2K4 | ENST00000353533.10 | c.*728dup | 3_prime_UTR_variant | 11/11 | 1 | NM_003010.4 | P2 | ||
MAP2K4 | ENST00000415385.7 | c.*728dup | 3_prime_UTR_variant | 12/12 | 2 | A2 | |||
MAP2K4 | ENST00000536413.2 | n.2110dup | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0205 AC: 3125AN: 152162Hom.: 36 Cov.: 32
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GnomAD4 exome AF: 0.0212 AC: 1716AN: 81080Hom.: 23 Cov.: 0 AF XY: 0.0202 AC XY: 754AN XY: 37314
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GnomAD4 genome AF: 0.0206 AC: 3132AN: 152280Hom.: 36 Cov.: 32 AF XY: 0.0209 AC XY: 1556AN XY: 74468
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ClinVar
Not reported inComputational scores
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at