rs1033706

Variant names:

• chr14-30180570-G-A
• rs1033706
• ENST00000508469.2:n.399-12213C>T

Your query was ambiguous. Multiple possible variants found:

• chr14-30180570-G-A
• chr14-30180570-G-C
• chr14-30180570-G-T

Variant summary

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

The ENST00000549503.1(PRKD1):​c.-46+10729C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,060 control chromosomes in the GnomAD database, including 41,419 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 0.73 (41419 hom., cov: 32)
• Consequence: PRKD1 ENST00000549503.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

Genes affected

ENSG00000248975 (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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.837 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
ENSG00000248975	ENST00000508469.2	n.399-12213C>T		intron_variant	Intron 3 of 3	1
PRKD1	ENST00000549503.1	c.-46+10729C>T		intron_variant	Intron 2 of 5	3		ENSP00000446866.1
ENSG00000248975	ENST00000549360.1	n.84+116364C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111539 AN: 151942 Hom.: 41381 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.734 AC: 111627 AN: 152060 Hom.: 41419 Cov.: 32 AF XY: 0.728 AC XY: 54125 AN XY: 74300

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.692

Alfa AF: 0.701 Hom.: 32822

Bravo AF: 0.741

Asia WGS AF: 0.767 AC: 2667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033706; hg19: chr14-30649776;