rs2154754

chr11-77467653-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002576.5(PAK1):c.-22+5899C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 151,876 control chromosomes in the GnomAD database, including 11,228 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 0.37 (11228 hom., cov: 32)
• Consequence: PAK1 NM_002576.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454

Genes affected

PAK1 (HGNC:8590): (p21 (RAC1) activated kinase 1) This gene encodes a family member of serine/threonine p21-activating kinases, known as PAK proteins. These proteins are critical effectors that link RhoGTPases to cytoskeleton reorganization and nuclear signaling, and they serve as targets for the small GTP binding proteins Cdc42 and Rac. This specific family member regulates cell motility and morphology. Mutations in this gene have been associated with macrocephaly, seizures, and speech delay. Overexpression of this gene is also reported in many cancer types, and particularly in breast cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.52 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAK1	NM_002576.5	c.-22+5899C>T		intron_variant		ENST00000356341.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAK1	ENST00000356341.8	c.-22+5899C>T		intron_variant		1	NM_002576.5	P1

Frequencies

GnomAD3 genomes AF: 0.369 AC: 56033 AN: 151754 Hom.: 11203 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.149

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.363

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.369 AC: 56100 AN: 151876 Hom.: 11228 Cov.: 32 AF XY: 0.369 AC XY: 27364 AN XY: 74242

Gnomad4 AFR AF: 0.526

Gnomad4 AMR AF: 0.289

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.400

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.362

Alfa AF: 0.320 Hom.: 13798

Bravo AF: 0.368

Asia WGS AF: 0.237 AC: 825 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	9.4
Dann	Benign	0.59

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

Other links and lift over

dbSNP: rs2154754; hg19: chr11-77178698;