rs8008553

chr14-29828885-G-Achr14-29828885-G-T

Variant summary

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

The NM_002742.3(PRKD1):c.264+98364C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,088 control chromosomes in the GnomAD database, including 41,101 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 0.73 (41101 hom., cov: 32)
• Consequence: PRKD1 NM_002742.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.127

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKD1	NM_002742.3	c.264+98364C>T		intron_variant		ENST00000331968.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKD1	ENST00000331968.11	c.264+98364C>T		intron_variant		1	NM_002742.3	P3
PRKD1	ENST00000415220.6	c.264+98364C>T		intron_variant		5		A1
PRKD1	ENST00000549503.1	c.34-103211C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111607 AN: 151970 Hom.: 41070 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.752

Gnomad ASJ AF: 0.742

Gnomad EAS AF: 0.740

Gnomad SAS AF: 0.741

Gnomad FIN AF: 0.722

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.734 AC: 111690 AN: 152088 Hom.: 41101 Cov.: 32 AF XY: 0.733 AC XY: 54511 AN XY: 74342

Gnomad4 AFR AF: 0.722

Gnomad4 AMR AF: 0.753

Gnomad4 ASJ AF: 0.742

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.722

Gnomad4 NFE AF: 0.740

Gnomad4 OTH AF: 0.730

Alfa AF: 0.739 Hom.: 23412

Bravo AF: 0.734

Asia WGS AF: 0.732 AC: 2547 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.4
Dann	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs8008553; hg19: chr14-30298091;