rs225848

Variant summary

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

The ENST00000549503.1(PRKD1):​c.-46+65848C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.916 in 152,224 control chromosomes in the GnomAD database, including 63,947 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 0.92 ( 63947 hom., cov: 32)

Consequence

PRKD1
ENST00000549503.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.58
Variant links:
Genes affected
PRKD1 (HGNC:9407): (protein kinase D1) The protein encoded by this gene is a serine/threonine protein kinase involved in many cellular processes, including Golgi body membrane integrity and transport, cell migration and differentiation, MAPK8/JNK1 and Ras pathway signaling, MAPK1/3 (ERK1/2) pathway signaling, cell survival, and regulation of cell shape and adhesion. [provided by RefSeq, Jan 2017]

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=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRKD1ENST00000549503.1 linkc.-46+65848C>T intron_variant Intron 2 of 5 3 ENSP00000446866.1 F8VZ98
ENSG00000248975ENST00000549360.1 linkn.85-145184C>T intron_variant Intron 1 of 2 3

Frequencies

GnomAD3 genomes
AF:
0.916
AC:
139386
AN:
152106
Hom.:
63909
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.897
Gnomad AMI
AF:
0.918
Gnomad AMR
AF:
0.937
Gnomad ASJ
AF:
0.936
Gnomad EAS
AF:
0.974
Gnomad SAS
AF:
0.969
Gnomad FIN
AF:
0.856
Gnomad MID
AF:
0.930
Gnomad NFE
AF:
0.923
Gnomad OTH
AF:
0.918
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.916
AC:
139480
AN:
152224
Hom.:
63947
Cov.:
32
AF XY:
0.915
AC XY:
68047
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.897
Gnomad4 AMR
AF:
0.937
Gnomad4 ASJ
AF:
0.936
Gnomad4 EAS
AF:
0.974
Gnomad4 SAS
AF:
0.968
Gnomad4 FIN
AF:
0.856
Gnomad4 NFE
AF:
0.923
Gnomad4 OTH
AF:
0.917
Alfa
AF:
0.922
Hom.:
20299
Bravo
AF:
0.921
Asia WGS
AF:
0.968
AC:
3368
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
15
DANN
Benign
0.43

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: rs225848; hg19: chr14-30594657; API