chr4-85992135-A-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001025616.3(ARHGAP24):c.929-2448A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000814 in 245,650 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 0.0000081 ( 0 hom. )
Consequence
ARHGAP24
NM_001025616.3 intron
NM_001025616.3 intron
Scores
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.05
Publications
0 publications found
Genes affected
ARHGAP24 (HGNC:25361): (Rho GTPase activating protein 24) This gene encodes a Rho-GTPase activating protein, which is specific for the small GTPase family member Rac. Binding of the encoded protein by filamin A targets it to sites of membrane protrusion, where it antognizes Rac. This results in suppression of lamellae formation and promotion of retraction to regulate cell polarity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2016]
MAPK10 (HGNC:6872): (mitogen-activated protein kinase 10) The protein encoded by this gene is a member of the MAP kinase family. MAP kinases act as integration points for multiple biochemical signals, and thus are involved in a wide variety of cellular processes, such as proliferation, differentiation, transcription regulation and development. This kinase is specifically expressed in a subset of neurons in the nervous system, and is activated by threonine and tyrosine phosphorylation. Targeted deletion of this gene in mice suggests that it may have a role in stress-induced neuronal apoptosis. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. A recent study provided evidence for translational readthrough in this gene, and expression of an additional C-terminally extended isoform via the use of an alternative in-frame translation termination codon. [provided by RefSeq, Dec 2017]
MAPK10 Gene-Disease associations (from GenCC):
- Lennox-Gastaut syndromeInheritance: AD Classification: LIMITED Submitted by: G2P
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000814 AC: 2AN: 245650Hom.: 0 Cov.: 0 AF XY: 0.00000803 AC XY: 1AN XY: 124472 show subpopulations
GnomAD4 exome
AF:
AC:
2
AN:
245650
Hom.:
Cov.:
0
AF XY:
AC XY:
1
AN XY:
124472
show subpopulations
African (AFR)
AF:
AC:
0
AN:
7146
American (AMR)
AF:
AC:
1
AN:
7432
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
9216
East Asian (EAS)
AF:
AC:
1
AN:
22880
South Asian (SAS)
AF:
AC:
0
AN:
3028
European-Finnish (FIN)
AF:
AC:
0
AN:
20820
Middle Eastern (MID)
AF:
AC:
0
AN:
1290
European-Non Finnish (NFE)
AF:
AC:
0
AN:
157500
Other (OTH)
AF:
AC:
0
AN:
16338
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
FATHMM_MKL
Benign
N
PhyloP100
GERP RS
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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