rs10411262

Variant names:

• chr19-46702503-C-G
• rs10411262
• NM_016457.5:c.890-1391G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016457.5(PRKD2):​c.890-1391G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 151,838 control chromosomes in the GnomAD database, including 27,245 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 0.59 (27245 hom., cov: 31)
• Consequence: PRKD2 NM_016457.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.207
• Publications: 5 publications found

Genes affected

PRKD2 (HGNC:17293): (protein kinase D2) The protein encoded by this gene belongs to the protein kinase D (PKD) family of serine/threonine protein kinases. This kinase can be activated by phorbol esters as well as by gastrin via the cholecystokinin B receptor (CCKBR) in gastric cancer cells. It can bind to diacylglycerol (DAG) in the trans-Golgi network (TGN) and may regulate basolateral membrane protein exit from TGN. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKD2	NM_016457.5	c.890-1391G>C		intron_variant	Intron 5 of 17	ENST00000291281.9	NP_057541.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PRKD2	ENST00000291281.9	c.890-1391G>C		intron_variant	Intron 5 of 17	1	NM_016457.5	ENSP00000291281.3

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90258 AN: 151718 Hom.: 27222 Cov.: 31

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.595 AC: 90341 AN: 151838 Hom.: 27245 Cov.: 31 AF XY: 0.598 AC XY: 44321 AN XY: 74170

African (AFR) AF: 0.688 AC: 28513 AN: 41414

American (AMR) AF: 0.625 AC: 9532 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2228 AN: 3468

East Asian (EAS) AF: 0.353 AC: 1820 AN: 5150

South Asian (SAS) AF: 0.622 AC: 2994 AN: 4814

European-Finnish (FIN) AF: 0.539 AC: 5651 AN: 10486

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37604 AN: 67952

Other (OTH) AF: 0.616 AC: 1297 AN: 2106

Alfa AF: 0.578 Hom.: 3197

Bravo AF: 0.605

Asia WGS AF: 0.495 AC: 1722 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.66
PhyloP100		0.21
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10411262; hg19: chr19-47205760;