rs11847697

Positions:

• chr14-30045906-C-T

Variant summary

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

The ENST00000549360.1(ENSG00000248975):​n.85-65639G>A 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 0.128 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: ENST00000549360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.266

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=-0.94).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000549360.1	n.85-65639G>A		intron_variant, non_coding_transcript_variant		3
PRKD1	ENST00000549503.1	c.33+1804G>A		intron_variant		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;