rs6789365
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002577.4(PAK2):c.1489-238C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0792 in 96,220 control chromosomes in the GnomAD database, including 1,322 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 0.079 ( 1322 hom., cov: 25)
Consequence
PAK2
NM_002577.4 intron
NM_002577.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -5.99
Genes affected
PAK2 (HGNC:8591): (p21 (RAC1) activated kinase 2) The p21 activated kinases (PAK) are critical effectors that link Rho GTPases to cytoskeleton reorganization and nuclear signaling. The PAK proteins are a family of serine/threonine kinases that serve as targets for the small GTP binding proteins, CDC42 and RAC1, and have been implicated in a wide range of biological activities. The protein encoded by this gene is activated by proteolytic cleavage during caspase-mediated apoptosis, and may play a role in regulating the apoptotic events in the dying cell. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAK2 | NM_002577.4 | c.1489-238C>A | intron_variant | ENST00000327134.7 | |||
PAK2 | XM_011512870.3 | c.1489-238C>A | intron_variant | ||||
PAK2 | XM_047448218.1 | c.1489-238C>A | intron_variant | ||||
PAK2 | XM_047448219.1 | c.1489-238C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAK2 | ENST00000327134.7 | c.1489-238C>A | intron_variant | 2 | NM_002577.4 | P1 | |||
PAK2 | ENST00000426668.1 | c.579-238C>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0791 AC: 7607AN: 96144Hom.: 1317 Cov.: 25
GnomAD3 genomes
?
AF:
AC:
7607
AN:
96144
Hom.:
Cov.:
25
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: 0.0792 AC: 7621AN: 96220Hom.: 1322 Cov.: 25 AF XY: 0.0809 AC XY: 3789AN XY: 46838
GnomAD4 genome
?
AF:
AC:
7621
AN:
96220
Hom.:
Cov.:
25
AF XY:
AC XY:
3789
AN XY:
46838
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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