rs225918

Variant names:

• chr14-29974448-G-A
• rs225918
• ENST00000549503.1:c.33+73262C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000549503.1(PRKD1):​c.33+73262C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.669 in 151,942 control chromosomes in the GnomAD database, including 35,865 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 0.67 (35865 hom., cov: 32)
• Consequence: PRKD1 ENST00000549503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.326

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]

ENSG00000248975 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.761 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
PRKD1	ENST00000549503.1	c.33+73262C>T		intron_variant	Intron 3 of 5	3		ENSP00000446866.1
ENSG00000248975	ENST00000548124.1	n.106+5701C>T		intron_variant	Intron 1 of 1	3
ENSG00000248975	ENST00000549360.1	n.204-1215C>T		intron_variant	Intron 2 of 2	3
ENSG00000257904	ENST00000553082.1	n.446-5389G>A		intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes AF: 0.669 AC: 101550 AN: 151824 Hom.: 35860 Cov.: 32

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.822

Gnomad MID AF: 0.675

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.673

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.669 AC: 101581 AN: 151942 Hom.: 35865 Cov.: 32 AF XY: 0.673 AC XY: 50030 AN XY: 74298

Gnomad4 AFR AF: 0.420

Gnomad4 AMR AF: 0.738

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.822

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.669

Alfa AF: 0.744 Hom.: 18891

Bravo AF: 0.652

Asia WGS AF: 0.697 AC: 2426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.64
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs225918; hg19: chr14-30443654;