chr14-30001469-C-A

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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+46241G>T		intron_variant	Intron 3 of 5	3		ENSP00000446866.1
ENSG00000248975	ENST00000549360.1	n.85-21202G>T		intron_variant	Intron 1 of 2	3

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

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.746

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225889; hg19: chr14-30470675;