rs225998

chr14-30021156-A-C

Variant summary

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

The ENST00000549360.1(ENSG00000248975):n.85-40889T>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,044 control chromosomes in the GnomAD database, including 5,462 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 0.26 (5462 hom., cov: 32)
• Consequence: ENST00000549360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0560

Genes affected

(HGNC:):

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.415 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000549360.1	n.85-40889T>G		intron_variant, non_coding_transcript_variant		3
PRKD1	ENST00000549503.1	c.33+26554T>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40248 AN: 151926 Hom.: 5461 Cov.: 32

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.112

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.431

Gnomad SAS AF: 0.314

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.265 AC: 40272 AN: 152044 Hom.: 5462 Cov.: 32 AF XY: 0.267 AC XY: 19819 AN XY: 74328

Gnomad4 AFR AF: 0.262

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.301

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.314

Gnomad4 FIN AF: 0.305

Gnomad4 NFE AF: 0.243

Gnomad4 OTH AF: 0.291

Alfa AF: 0.253 Hom.: 584

Bravo AF: 0.264

Asia WGS AF: 0.378 AC: 1311 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	1.5
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225998; hg19: chr14-30490362;