X-3656497-A-G

Variant summary

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

The NM_005044.5(PRKX):​c.336-1085T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 110,384 control chromosomes in the GnomAD database, including 4,439 homozygotes. There are 10,196 hemizygotes in GnomAD. 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 0.32 ( 4439 hom., 10196 hem., cov: 22)

Consequence

PRKX
NM_005044.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.03
Variant links:
Genes affected
PRKX (HGNC:9441): (protein kinase cAMP-dependent X-linked catalytic subunit) This gene encodes a serine threonine protein kinase that has similarity to the catalytic subunit of cyclic AMP dependent protein kinases. The encoded protein is developmentally regulated and may be involved in renal epithelial morphogenesis. This protein may also be involved in macrophage and granulocyte maturation. Abnormal recombination between this gene and a related pseudogene on chromosome Y is a frequent cause of sex reversal disorder in XX males and XY females. Pseudogenes of this gene are found on chromosomes X, 15 and Y. [provided by RefSeq, Feb 2010]

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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=-0.96).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.581 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PRKXNM_005044.5 linkc.336-1085T>C intron_variant Intron 2 of 8 ENST00000262848.6 NP_005035.1 P51817A0A024RBU5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRKXENST00000262848.6 linkc.336-1085T>C intron_variant Intron 2 of 8 1 NM_005044.5 ENSP00000262848.5 P51817
PRKXENST00000425240.1 linkn.38-1085T>C intron_variant Intron 1 of 6 5

Frequencies

GnomAD3 genomes
AF:
0.319
AC:
35241
AN:
110332
Hom.:
4428
Cov.:
22
AF XY:
0.311
AC XY:
10164
AN XY:
32672
show subpopulations
Gnomad AFR
AF:
0.200
Gnomad AMI
AF:
0.395
Gnomad AMR
AF:
0.465
Gnomad ASJ
AF:
0.403
Gnomad EAS
AF:
0.602
Gnomad SAS
AF:
0.441
Gnomad FIN
AF:
0.240
Gnomad MID
AF:
0.328
Gnomad NFE
AF:
0.337
Gnomad OTH
AF:
0.379
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.320
AC:
35288
AN:
110384
Hom.:
4439
Cov.:
22
AF XY:
0.311
AC XY:
10196
AN XY:
32734
show subpopulations
Gnomad4 AFR
AF:
0.200
Gnomad4 AMR
AF:
0.466
Gnomad4 ASJ
AF:
0.403
Gnomad4 EAS
AF:
0.603
Gnomad4 SAS
AF:
0.440
Gnomad4 FIN
AF:
0.240
Gnomad4 NFE
AF:
0.337
Gnomad4 OTH
AF:
0.388
Alfa
AF:
0.326
Hom.:
4247
Bravo
AF:
0.338

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.83
DANN
Benign
0.13

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: rs17335275; hg19: chrX-3574538; API