18-50664141-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_002747.4(MAPK4):c.183C>T(p.His61His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00447 in 1,614,168 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0042 ( 3 hom., cov: 32)
Exomes 𝑓: 0.0045 ( 20 hom. )
Consequence
MAPK4
NM_002747.4 synonymous
NM_002747.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.70
Genes affected
MAPK4 (HGNC:6878): (mitogen-activated protein kinase 4) Mitogen-activated protein kinase 4 is a member of the mitogen-activated protein kinase family. Tyrosine kinase growth factor receptors activate mitogen-activated protein kinases which then translocate into the nucleus and phosphorylate nuclear targets. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -11 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.67).
BP6
Variant 18-50664141-C-T is Benign according to our data. Variant chr18-50664141-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648718.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.7 with no splicing effect.
BS2
High AC in GnomAd4 at 644 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00423 AC: 644AN: 152206Hom.: 3 Cov.: 32
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GnomAD3 exomes AF: 0.00387 AC: 964AN: 249370Hom.: 4 AF XY: 0.00416 AC XY: 563AN XY: 135302
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GnomAD4 exome AF: 0.00450 AC: 6577AN: 1461844Hom.: 20 Cov.: 34 AF XY: 0.00454 AC XY: 3300AN XY: 727224
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GnomAD4 genome AF: 0.00423 AC: 644AN: 152324Hom.: 3 Cov.: 32 AF XY: 0.00474 AC XY: 353AN XY: 74480
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Jan 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
MAPK4: BP4, BP7, BS2 -
Computational scores
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Name
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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