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. The variant received -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
• Publications: 3 publications found

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]

PRKD1 Gene-Disease associations (from GenCC):

• congenital heart defects and ectodermal dysplasia

  Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
• congenital heart defects, multiple types

  Inheritance: AR Classification: MODERATE Submitted by: Ambry Genetics
• complex neurodevelopmental disorder

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• congenital heart disease

  Inheritance: AR, AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000549503.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000248975	ENST00000508469.2	TSL:1	n.399-12213C>T		intron	N/A
	PRKD1	ENST00000549503.1	TSL:3	c.-46+10729C>T		intron	N/A	ENSP00000446866.1	F8VZ98
	ENSG00000248975	ENST00000549360.1	TSL:3	n.84+116364C>T		intron	N/A

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

African (AFR) AF: 0.844 AC: 35081 AN: 41546

American (AMR) AF: 0.651 AC: 9944 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2542 AN: 3472

East Asian (EAS) AF: 0.739 AC: 3802 AN: 5146

South Asian (SAS) AF: 0.751 AC: 3617 AN: 4816

European-Finnish (FIN) AF: 0.613 AC: 6464 AN: 10540

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47793 AN: 67954

Other (OTH) AF: 0.692 AC: 1463 AN: 2114

Alfa AF: 0.709 Hom.: 45418

Bravo AF: 0.741

Asia WGS AF: 0.767 AC: 2667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.51
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs1033706; hg19: chr14-30649776;