chr14-29897406-A-G

Position:

• chr14-29897406-A-G

Variant summary

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

The NM_002742.3(PRKD1):​c.264+29843T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0649 in 152,222 control chromosomes in the GnomAD database, including 395 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 0.065 (395 hom., cov: 32)
• Consequence: PRKD1 NM_002742.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.672

Genes affected

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=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRKD1	NM_002742.3	c.264+29843T>C		intron_variant		ENST00000331968.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRKD1	ENST00000331968.11	c.264+29843T>C		intron_variant		1	NM_002742.3	P3
PRKD1	ENST00000415220.6	c.264+29843T>C		intron_variant		5		A1
PRKD1	ENST00000549503.1	c.33+150304T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0649 AC: 9867 AN: 152106 Hom.: 391 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0480

Gnomad ASJ AF: 0.0965

Gnomad EAS AF: 0.0815

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0691

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

GnomAD4 genome AF: 0.0649 AC: 9883 AN: 152222 Hom.: 395 Cov.: 32 AF XY: 0.0665 AC XY: 4953 AN XY: 74440

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.0479

Gnomad4 ASJ AF: 0.0965

Gnomad4 EAS AF: 0.0819

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.0360

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0712

Alfa AF: 0.0519 Hom.: 32

Bravo AF: 0.0661

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs17096124; hg19: chr14-30366612;