rs225830

chr14-30071535-G-Achr14-30071535-G-C

Variant summary

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

The ENST00000549360.1(ENSG00000248975):n.85-91268C>T 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 0.603 in 152,040 control chromosomes in the GnomAD database, including 27,942 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 0.60 (27942 hom., cov: 33)
• Consequence: ENST00000549360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000549360.1	n.85-91268C>T		intron_variant, non_coding_transcript_variant		3
PRKD1	ENST00000549503.1	c.-45-23748C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.603 AC: 91601 AN: 151924 Hom.: 27927 Cov.: 33

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.620

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.578

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.603 AC: 91667 AN: 152040 Hom.: 27942 Cov.: 33 AF XY: 0.606 AC XY: 45043 AN XY: 74302

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.620

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.585

Alfa AF: 0.496 Hom.: 1493

Bravo AF: 0.609

Asia WGS AF: 0.748 AC: 2600 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	7.7
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225830; hg19: chr14-30540741;