14-30137220-T-G

Position:

• chr14-30137220-T-G

Variant summary

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

The ENST00000549503.1(PRKD1):​c.-46+54079A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.367 in 151,968 control chromosomes in the GnomAD database, including 11,231 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 0.37 (11231 hom., cov: 32)
• Consequence: PRKD1 ENST00000549503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.116

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=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.30137220T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKD1	ENST00000549503.1	c.-46+54079A>C		intron_variant		3		ENSP00000446866.1
ENSG00000248975	ENST00000549360.1	n.85-156953A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55805 AN: 151850 Hom.: 11228 Cov.: 32

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.00541

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.327

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.367 AC: 55835 AN: 151968 Hom.: 11231 Cov.: 32 AF XY: 0.363 AC XY: 26927 AN XY: 74266

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.375

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.00562

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.327

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.342

Alfa AF: 0.357 Hom.: 1492

Bravo AF: 0.376

Asia WGS AF: 0.112 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8019932; hg19: chr14-30606426;