rs225889

Positions:

• chr14-30001469-C-A
• chr14-30001469-C-G
• chr14-30001469-C-T

Variant summary

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

The ENST00000549360.1(ENSG00000248975):​n.85-21202G>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 0.737 in 152,080 control chromosomes in the GnomAD database, including 42,197 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 0.74 (42197 hom., cov: 32)
• Consequence: ENST00000549360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.855 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.85-21202G>T		intron_variant, non_coding_transcript_variant		3
PRKD1	ENST00000549503.1	c.33+46241G>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.738 AC: 112107 AN: 151962 Hom.: 42183 Cov.: 32

Gnomad AFR AF: 0.577

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.755

Gnomad EAS AF: 0.876

Gnomad SAS AF: 0.789

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.806

Gnomad OTH AF: 0.748

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

GnomAD4 genome AF: 0.737 AC: 112151 AN: 152080 Hom.: 42197 Cov.: 32 AF XY: 0.736 AC XY: 54722 AN XY: 74334

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.778

Gnomad4 ASJ AF: 0.755

Gnomad4 EAS AF: 0.876

Gnomad4 SAS AF: 0.789

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.806

Gnomad4 OTH AF: 0.746

Alfa AF: 0.773 Hom.: 5713

Bravo AF: 0.730

Asia WGS AF: 0.803 AC: 2793 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225889; hg19: chr14-30470675;