rs225889

Variant names:

• chr14-30001469-C-A
• rs225889
• ENST00000549503.1:c.33+46241G>T

Your query was ambiguous. Multiple possible variants found:

• chr14-30001469-C-A
• chr14-30001469-C-G
• chr14-30001469-C-T

Variant summary

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

The ENST00000549503.1(PRKD1):​c.33+46241G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 152,080 control chromosomes in the GnomAD database, including 42,197 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 0.74 (42197 hom., cov: 32)
• Consequence: PRKD1 ENST00000549503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 1 publications found

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]

PRKD1 Gene-Disease associations (from GenCC):

• congenital heart defects and ectodermal dysplasia

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• congenital heart defects, multiple types

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

ENSG00000248975 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549503.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRKD1	ENST00000549503.1	TSL:3	c.33+46241G>T		intron	N/A	ENSP00000446866.1
	ENSG00000248975	ENST00000549360.1	TSL:3	n.85-21202G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112107 AN: 151962 Hom.: 42183 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.737 AC: 112151 AN: 152080 Hom.: 42197 Cov.: 32 AF XY: 0.736 AC XY: 54722 AN XY: 74334

African (AFR) AF: 0.576 AC: 23872 AN: 41448

American (AMR) AF: 0.778 AC: 11896 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.755 AC: 2620 AN: 3470

East Asian (EAS) AF: 0.876 AC: 4529 AN: 5170

South Asian (SAS) AF: 0.789 AC: 3803 AN: 4818

European-Finnish (FIN) AF: 0.778 AC: 8230 AN: 10580

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.806 AC: 54794 AN: 67990

Other (OTH) AF: 0.746 AC: 1578 AN: 2116

Alfa AF: 0.773 Hom.: 5713

Bravo AF: 0.730

Asia WGS AF: 0.803 AC: 2793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.27
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs225889; hg19: chr14-30470675;