rs11711261

Variant names:

• chr3-58357969-C-A
• rs11711261
• NM_017771.5:c.103-7905C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-58357969-C-A
• chr3-58357969-C-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.879
• Publications: 2 publications found

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]

PXK Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017771.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PXK	NM_017771.5	MANE Select	c.103-7905C>A		intron	N/A	NP_060241.2
	PXK	NM_001349492.2		c.103-7905C>A		intron	N/A	NP_001336421.1
	PXK	NM_001349493.2		c.103-7905C>A		intron	N/A	NP_001336422.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PXK	ENST00000356151.7	TSL:1 MANE Select	c.103-7905C>A		intron	N/A	ENSP00000348472.2	Q7Z7A4-1
	PXK	ENST00000302779.9	TSL:1	c.103-7905C>A		intron	N/A	ENSP00000305045.6	W5RWE6
	PXK	ENST00000383716.7	TSL:1	c.103-7905C>A		intron	N/A	ENSP00000373222.4	Q7Z7A4-2

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33251 AN: 150262 Hom.: 4738 Cov.: 31

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

African (AFR) AF: 0.395 AC: 16066 AN: 40718

American (AMR) AF: 0.142 AC: 2153 AN: 15146

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3458

East Asian (EAS) AF: 0.00156 AC: 8 AN: 5126

South Asian (SAS) AF: 0.158 AC: 754 AN: 4778

European-Finnish (FIN) AF: 0.170 AC: 1744 AN: 10250

Middle Eastern (MID) AF: 0.151 AC: 44 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11409 AN: 67606

Other (OTH) AF: 0.186 AC: 390 AN: 2094

Alfa AF: 0.0691 Hom.: 145

Bravo AF: 0.228

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.41
DANN	Benign	0.27
PhyloP100		-0.88
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11711261; hg19: chr3-58343696;