rs41305272
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000178640.10(MAP2K5):c.*355C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0319 in 572,126 control chromosomes in the GnomAD database, including 372 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 0.024 ( 58 hom., cov: 33)
Exomes 𝑓: 0.035 ( 314 hom. )
Consequence
MAP2K5
ENST00000178640.10 3_prime_UTR
ENST00000178640.10 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.42
Genes affected
MAP2K5 (HGNC:6845): (mitogen-activated protein kinase kinase 5) The protein encoded by this gene is a dual specificity protein kinase that belongs to the MAP kinase kinase family. This kinase specifically interacts with and activates MAPK7/ERK5. This kinase itself can be phosphorylated and activated by MAP3K3/MEKK3, as well as by atypical protein kinase C isoforms (aPKCs). The signal cascade mediated by this kinase is involved in growth factor stimulated cell proliferation and muscle cell differentiation. Three alternatively spliced transcript variants of this gene encoding distinct isoforms have been described. [provided by RefSeq, May 2011]
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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=-0.51).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0238 (3625/152330) while in subpopulation NFE AF= 0.0401 (2725/68022). AF 95% confidence interval is 0.0388. There are 58 homozygotes in gnomad4. There are 1651 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 3625 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAP2K5 | NM_145160.3 | c.*355C>T | 3_prime_UTR_variant | 22/22 | ENST00000178640.10 | NP_660143.1 | ||
MAP2K5 | NM_001206804.2 | c.*355C>T | 3_prime_UTR_variant | 22/22 | NP_001193733.1 | |||
MAP2K5 | NM_002757.4 | c.*355C>T | 3_prime_UTR_variant | 21/21 | NP_002748.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAP2K5 | ENST00000178640.10 | c.*355C>T | 3_prime_UTR_variant | 22/22 | 1 | NM_145160.3 | ENSP00000178640 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0238 AC: 3627AN: 152212Hom.: 59 Cov.: 33
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GnomAD4 exome AF: 0.0348 AC: 14610AN: 419796Hom.: 314 Cov.: 7 AF XY: 0.0333 AC XY: 7119AN XY: 213960
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GnomAD4 genome AF: 0.0238 AC: 3625AN: 152330Hom.: 58 Cov.: 33 AF XY: 0.0222 AC XY: 1651AN XY: 74490
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at