rs225830

Variant names:

• chr14-30071535-G-A
• rs225830
• ENST00000549503.1:c.-45-23748C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-30071535-G-A
• chr14-30071535-G-C

Variant summary

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

The ENST00000549503.1(PRKD1):​c.-45-23748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.603 in 152,040 control chromosomes in the GnomAD database, including 27,942 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 0.60 (27942 hom., cov: 33)
• Consequence: PRKD1 ENST00000549503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 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.-45-23748C>T		intron_variant	Intron 2 of 5	3		ENSP00000446866.1
ENSG00000248975	ENST00000549360.1	n.85-91268C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91601 AN: 151924 Hom.: 27927 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.603 AC: 91667 AN: 152040 Hom.: 27942 Cov.: 33 AF XY: 0.606 AC XY: 45043 AN XY: 74302

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.585

Alfa AF: 0.496 Hom.: 1493

Bravo AF: 0.609

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	7.7
DANN	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225830; hg19: chr14-30540741;