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GeneBe

rs16970458

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001395430.1(PAK6):​c.-118+2097T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 152,022 control chromosomes in the GnomAD database, including 25,358 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 0.56 ( 25358 hom., cov: 32)

Consequence

PAK6
NM_001395430.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.34
Variant links:
Genes affected
PAK6 (HGNC:16061): (p21 (RAC1) activated kinase 6) This gene encodes a member of a family of p21-stimulated serine/threonine protein kinases, which contain an amino-terminal Cdc42/Rac interactive binding (CRIB) domain and a carboxyl-terminal kinase domain. These kinases function in a number of cellular processes, including cytoskeleton rearrangement, apoptosis, and the mitogen-activated protein (MAP) kinase signaling pathway. The protein encoded by this gene interacts with androgen receptor (AR) and translocates to the nucleus, where it is involved in transcriptional regulation. Changes in expression of this gene have been linked to prostate cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PAK6NM_001395430.1 linkuse as main transcriptc.-118+2097T>C intron_variant ENST00000560346.6
BUB1B-PAK6NM_001128628.3 linkuse as main transcriptc.-118+2097T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PAK6ENST00000560346.6 linkuse as main transcriptc.-118+2097T>C intron_variant 5 NM_001395430.1 P1Q9NQU5-1

Frequencies

GnomAD3 genomes
AF:
0.556
AC:
84411
AN:
151902
Hom.:
25357
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.356
Gnomad AMI
AF:
0.721
Gnomad AMR
AF:
0.494
Gnomad ASJ
AF:
0.749
Gnomad EAS
AF:
0.252
Gnomad SAS
AF:
0.511
Gnomad FIN
AF:
0.630
Gnomad MID
AF:
0.604
Gnomad NFE
AF:
0.692
Gnomad OTH
AF:
0.581
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.555
AC:
84414
AN:
152022
Hom.:
25358
Cov.:
32
AF XY:
0.549
AC XY:
40819
AN XY:
74318
show subpopulations
Gnomad4 AFR
AF:
0.356
Gnomad4 AMR
AF:
0.493
Gnomad4 ASJ
AF:
0.749
Gnomad4 EAS
AF:
0.252
Gnomad4 SAS
AF:
0.511
Gnomad4 FIN
AF:
0.630
Gnomad4 NFE
AF:
0.692
Gnomad4 OTH
AF:
0.579
Alfa
AF:
0.656
Hom.:
31997
Bravo
AF:
0.534
Asia WGS
AF:
0.379
AC:
1322
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
0.028
DANN
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs16970458; hg19: chr15-40534979; API