rs10498313

chr14-29929670-A-G

Variant summary

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

The ENST00000654897.1(ENSG00000287142):n.667+559A>G 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 0.187 in 152,116 control chromosomes in the GnomAD database, including 2,813 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 0.19 (2813 hom., cov: 32)
• Consequence: ENST00000654897.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.417

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370429	XR_943703.2	n.985+559A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654897.1	n.667+559A>G		intron_variant, non_coding_transcript_variant
PRKD1	ENST00000549503.1	c.33+118040T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.187 AC: 28368 AN: 151998 Hom.: 2811 Cov.: 32

Gnomad AFR AF: 0.146

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.206

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.163

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.138

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.210

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

GnomAD4 genome AF: 0.187 AC: 28396 AN: 152116 Hom.: 2813 Cov.: 32 AF XY: 0.185 AC XY: 13728 AN XY: 74358

Gnomad4 AFR AF: 0.146

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.225

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.138

Gnomad4 NFE AF: 0.213

Gnomad4 OTH AF: 0.212

Alfa AF: 0.202 Hom.: 2337

Bravo AF: 0.188

Asia WGS AF: 0.173 AC: 601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	4.4
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10498313; hg19: chr14-30398876;