14-30117690-C-T

Position:

• chr14-30117690-C-T

Variant summary

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

The ENST00000549503.1(PRKD1):​c.-45-69903G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,052 control chromosomes in the GnomAD database, including 63,525 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 0.91 (63525 hom., cov: 30)
• Consequence: PRKD1 ENST00000549503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.35

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• 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/exons	MANE	Protein	UniProt
		n.30117690C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKD1	ENST00000549503.1	c.-45-69903G>A		intron_variant		3		ENSP00000446866.1
ENSG00000248975	ENST00000549360.1	n.85-137423G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138849 AN: 151934 Hom.: 63495 Cov.: 30

Gnomad AFR AF: 0.889

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.916

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

GnomAD4 genome AF: 0.914 AC: 138932 AN: 152052 Hom.: 63525 Cov.: 30 AF XY: 0.912 AC XY: 67790 AN XY: 74320

Gnomad4 AFR AF: 0.888

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: 0.916

Alfa AF: 0.918 Hom.: 13015

Bravo AF: 0.918

Asia WGS AF: 0.967 AC: 3364 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.53
DANN	Benign	0.32
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225858; hg19: chr14-30586896;