rs252902
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_005921.2(MAP3K1):c.482+4203A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.775 in 176,670 control chromosomes in the GnomAD database, including 53,408 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.77 ( 45375 hom., cov: 31)
Exomes 𝑓: 0.81 ( 8033 hom. )
Consequence
MAP3K1
NM_005921.2 intron
NM_005921.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0660
Genes affected
MAP3K1 (HGNC:6848): (mitogen-activated protein kinase kinase kinase 1) The protein encoded by this gene is a serine/threonine kinase and is part of some signal transduction cascades, including the ERK and JNK kinase pathways as well as the NF-kappa-B pathway. The encoded protein is activated by autophosphorylation and requires magnesium as a cofactor in phosphorylating other proteins. This protein has E3 ligase activity conferred by a plant homeodomain (PHD) in its N-terminus and phospho-kinase activity conferred by a kinase domain in its C-terminus. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.815 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MAP3K1 | NM_005921.2 | c.482+4203A>G | intron_variant | ENST00000399503.4 | |||
MAP3K1 | XM_047417219.1 | c.-488A>G | 5_prime_UTR_variant | 2/21 | |||
MAP3K1 | XM_047417218.1 | c.482+4203A>G | intron_variant | ||||
MAP3K1 | XM_047417220.1 | c.-20-468A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MAP3K1 | ENST00000399503.4 | c.482+4203A>G | intron_variant | 1 | NM_005921.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.770 AC: 116864AN: 151828Hom.: 45323 Cov.: 31
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GnomAD4 exome AF: 0.806 AC: 19922AN: 24724Hom.: 8033 AF XY: 0.806 AC XY: 9645AN XY: 11964
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GnomAD4 genome AF: 0.770 AC: 116970AN: 151946Hom.: 45375 Cov.: 31 AF XY: 0.765 AC XY: 56828AN XY: 74264
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at