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rs2105803

Variant summary

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

The XM_024448560.2(PAK1):c.-377+6982T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.254 in 152,116 control chromosomes in the GnomAD database, including 5,455 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 0.25 ( 5455 hom., cov: 33)

Consequence

PAK1
XM_024448560.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.231
Variant links:
Genes affected
CLNS1A (HGNC:2080): (chloride nucleotide-sensitive channel 1A) This gene encodes a protein that functions in multiple regulatory pathways. The encoded protein complexes with numerous cytosolic proteins and performs diverse functions including regulation of small nuclear ribonucleoprotein biosynthesis, platelet activation and cytoskeletal organization. The protein is also found associated with the plasma membrane where it functions as a chloride current regulator. Pseudogenes of this gene are found on chromosomes 1, 4 and 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 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 (SAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PAK1XM_024448560.2 linkuse as main transcriptc.-377+6982T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLNS1AENST00000526761.5 linkuse as main transcriptc.*320+6982T>C intron_variant, NMD_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.254
AC:
38646
AN:
151996
Hom.:
5442
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.236
Gnomad AMI
AF:
0.469
Gnomad AMR
AF:
0.413
Gnomad ASJ
AF:
0.278
Gnomad EAS
AF:
0.318
Gnomad SAS
AF:
0.485
Gnomad FIN
AF:
0.201
Gnomad MID
AF:
0.377
Gnomad NFE
AF:
0.212
Gnomad OTH
AF:
0.246
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.254
AC:
38704
AN:
152116
Hom.:
5455
Cov.:
33
AF XY:
0.262
AC XY:
19489
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.236
Gnomad4 AMR
AF:
0.414
Gnomad4 ASJ
AF:
0.278
Gnomad4 EAS
AF:
0.319
Gnomad4 SAS
AF:
0.485
Gnomad4 FIN
AF:
0.201
Gnomad4 NFE
AF:
0.212
Gnomad4 OTH
AF:
0.248
Alfa
AF:
0.253
Hom.:
898
Bravo
AF:
0.264
Asia WGS
AF:
0.423
AC:
1471
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
4.5
Dann
Benign
0.52

Splicing

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: rs2105803; hg19: chr11-77234011; API