rs10144903

Positions:

• chr14-29803103-T-G

Variant summary

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

The NM_002742.3(PRKD1):​c.265-77429A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 152,058 control chromosomes in the GnomAD database, including 3,891 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 0.22 (3891 hom., cov: 32)
• Consequence: PRKD1 NM_002742.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.05

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKD1	NM_002742.3	c.265-77429A>C		intron_variant		ENST00000331968.11	NP_002733.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKD1	ENST00000331968.11	c.265-77429A>C		intron_variant		1	NM_002742.3	ENSP00000333568.6
PRKD1	ENST00000415220.6	c.265-77429A>C		intron_variant		5		ENSP00000390535.2
PRKD1	ENST00000549503.1	c.34-77429A>C		intron_variant		3		ENSP00000446866.1

Frequencies

GnomAD3 genomes AF: 0.217 AC: 32951 AN: 151938 Hom.: 3867 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.0868

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.217 AC: 33025 AN: 152058 Hom.: 3891 Cov.: 32 AF XY: 0.215 AC XY: 15973 AN XY: 74308

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.0870

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.178

Gnomad4 NFE AF: 0.201

Gnomad4 OTH AF: 0.213

Alfa AF: 0.198 Hom.: 6151

Bravo AF: 0.212

Asia WGS AF: 0.190 AC: 661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.058
DANN	Benign	0.44

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

Publications

LitVar

Other links and lift over

dbSNP: rs10144903; hg19: chr14-30272309;