rs225848

Positions:

• chr14-30125451-G-A
• chr14-30125451-G-T

Variant summary

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

The ENST00000549360.1(ENSG00000248975):​n.85-145184C>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 0.916 in 152,224 control chromosomes in the GnomAD database, including 63,947 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 0.92 (63947 hom., cov: 32)
• Consequence: ENST00000549360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.58

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.951 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.85-145184C>T		intron_variant, non_coding_transcript_variant		3
PRKD1	ENST00000549503.1	c.-46+65848C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.916 AC: 139386 AN: 152106 Hom.: 63909 Cov.: 32

Gnomad AFR AF: 0.897

Gnomad AMI AF: 0.918

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.936

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.969

Gnomad FIN AF: 0.856

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.916 AC: 139480 AN: 152224 Hom.: 63947 Cov.: 32 AF XY: 0.915 AC XY: 68047 AN XY: 74404

Gnomad4 AFR AF: 0.897

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.936

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.856

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.917

Alfa AF: 0.922 Hom.: 20299

Bravo AF: 0.921

Asia WGS AF: 0.968 AC: 3368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	15
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225848; hg19: chr14-30594657;