rs11711261

Variant summary

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

The NM_017771.5(PXK):​c.103-7905C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 150,366 control chromosomes in the GnomAD database, including 4,759 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 0.22 ( 4759 hom., cov: 31)

Consequence

PXK
NM_017771.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.879
Variant links:
Genes affected
PXK (HGNC:23326): (PX domain containing serine/threonine kinase like) This gene encodes a phox (PX) domain-containing protein which may be involved in synaptic transmission and the ligand-induced internalization and degradation of epidermal growth factors. Variations in this gene may be associated with susceptibility to systemic lupus erythematosus (SLE). Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PXKNM_017771.5 linkuse as main transcriptc.103-7905C>A intron_variant ENST00000356151.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PXKENST00000356151.7 linkuse as main transcriptc.103-7905C>A intron_variant 1 NM_017771.5 P1Q7Z7A4-1

Frequencies

GnomAD3 genomes
AF:
0.221
AC:
33251
AN:
150262
Hom.:
4738
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.394
Gnomad AMI
AF:
0.183
Gnomad AMR
AF:
0.143
Gnomad ASJ
AF:
0.165
Gnomad EAS
AF:
0.00156
Gnomad SAS
AF:
0.158
Gnomad FIN
AF:
0.170
Gnomad MID
AF:
0.162
Gnomad NFE
AF:
0.169
Gnomad OTH
AF:
0.189
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.221
AC:
33303
AN:
150366
Hom.:
4759
Cov.:
31
AF XY:
0.220
AC XY:
16151
AN XY:
73378
show subpopulations
Gnomad4 AFR
AF:
0.395
Gnomad4 AMR
AF:
0.142
Gnomad4 ASJ
AF:
0.165
Gnomad4 EAS
AF:
0.00156
Gnomad4 SAS
AF:
0.158
Gnomad4 FIN
AF:
0.170
Gnomad4 NFE
AF:
0.169
Gnomad4 OTH
AF:
0.186
Alfa
AF:
0.0501
Hom.:
72
Bravo
AF:
0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
0.41
DANN
Benign
0.27

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: rs11711261; hg19: chr3-58343696; API