18-50582393-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002747.4(MAPK4):c.-871+22150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 152,070 control chromosomes in the GnomAD database, including 37,519 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 0.70 ( 37519 hom., cov: 32)
Consequence
MAPK4
NM_002747.4 intron
NM_002747.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.209
Publications
3 publications found
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 was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPK4 | ENST00000400384.7 | c.-871+22150A>G | intron_variant | Intron 1 of 5 | 1 | NM_002747.4 | ENSP00000383234.1 | |||
MAPK4 | ENST00000588540.1 | c.-871+21634A>G | intron_variant | Intron 1 of 2 | 1 | ENSP00000465661.1 | ||||
MAPK4 | ENST00000592595.5 | c.-871+22150A>G | intron_variant | Intron 1 of 3 | 1 | ENSP00000466233.1 | ||||
MAPK4 | ENST00000540640.3 | c.-88+22150A>G | intron_variant | Intron 1 of 4 | 2 | ENSP00000439231.1 |
Frequencies
GnomAD3 genomes AF: 0.700 AC: 106402AN: 151952Hom.: 37512 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
106402
AN:
151952
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.700 AC: 106461AN: 152070Hom.: 37519 Cov.: 32 AF XY: 0.702 AC XY: 52164AN XY: 74330 show subpopulations
GnomAD4 genome
AF:
AC:
106461
AN:
152070
Hom.:
Cov.:
32
AF XY:
AC XY:
52164
AN XY:
74330
show subpopulations
African (AFR)
AF:
AC:
25382
AN:
41462
American (AMR)
AF:
AC:
11003
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
2535
AN:
3472
East Asian (EAS)
AF:
AC:
3858
AN:
5162
South Asian (SAS)
AF:
AC:
3227
AN:
4812
European-Finnish (FIN)
AF:
AC:
8224
AN:
10590
Middle Eastern (MID)
AF:
AC:
195
AN:
294
European-Non Finnish (NFE)
AF:
AC:
49907
AN:
67956
Other (OTH)
AF:
AC:
1522
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1629
3258
4886
6515
8144
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2405
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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