rs11847697

Variant names:

• chr14-30045906-C-T
• rs11847697
• ENST00000549503.1:c.33+1804G>A

Variant summary

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

The ENST00000549503.1(PRKD1):​c.33+1804G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 151,970 control chromosomes in the GnomAD database, including 2,634 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 0.13 (2634 hom., cov: 30)
• Consequence: PRKD1 ENST00000549503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 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.33+1804G>A		intron_variant	Intron 3 of 5	3		ENSP00000446866.1
ENSG00000248975	ENST00000549360.1	n.85-65639G>A		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19447 AN: 151852 Hom.: 2633 Cov.: 30

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.0712

Gnomad ASJ AF: 0.0482

Gnomad EAS AF: 0.00136

Gnomad SAS AF: 0.0906

Gnomad FIN AF: 0.0133

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0440

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.128 AC: 19470 AN: 151970 Hom.: 2634 Cov.: 30 AF XY: 0.126 AC XY: 9361 AN XY: 74276

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.0710

Gnomad4 ASJ AF: 0.0482

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0894

Gnomad4 FIN AF: 0.0133

Gnomad4 NFE AF: 0.0441

Gnomad4 OTH AF: 0.112

Alfa AF: 0.0548 Hom.: 628

Bravo AF: 0.142

Asia WGS AF: 0.0680 AC: 235 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	3.3
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11847697; hg19: chr14-30515112;