14-30180570-G-A

Position:

• chr14-30180570-G-A

Variant summary

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

The ENST00000508469.2(ENSG00000248975):​n.399-12213C>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 0.734 in 152,060 control chromosomes in the GnomAD database, including 41,419 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 0.73 (41419 hom., cov: 32)
• Consequence: ENST00000508469.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

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 (AFR) allele frequency at 95% confidence interval = 0.837 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000508469.2	n.399-12213C>T		intron_variant, non_coding_transcript_variant		1
	ENST00000549360.1	n.84+116364C>T		intron_variant, non_coding_transcript_variant		3
PRKD1	ENST00000549503.1	c.-46+10729C>T		intron_variant		3		ENSP00000446866

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111539 AN: 151942 Hom.: 41381 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.739

Gnomad SAS AF: 0.751

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.696

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

GnomAD4 genome AF: 0.734 AC: 111627 AN: 152060 Hom.: 41419 Cov.: 32 AF XY: 0.728 AC XY: 54125 AN XY: 74300

Gnomad4 AFR AF: 0.844

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.739

Gnomad4 SAS AF: 0.751

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.692

Alfa AF: 0.701 Hom.: 32822

Bravo AF: 0.741

Asia WGS AF: 0.767 AC: 2667 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1033706; hg19: chr14-30649776;