chr14-30056182-T-C

Position:

• chr14-30056182-T-C

Variant summary

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

The ENST00000549360.1(ENSG00000248975):​n.85-75915A>G 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 0.649 in 151,490 control chromosomes in the GnomAD database, including 32,344 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 0.65 (32344 hom., cov: 31)
• Consequence: ENST00000549360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0350

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=-0.72).
• 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	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000549360.1	n.85-75915A>G		intron_variant, non_coding_transcript_variant		3
PRKD1	ENST00000549503.1	c.-45-8395A>G		intron_variant		3		ENSP00000446866

Frequencies

GnomAD3 genomes AF: 0.648 AC: 98157 AN: 151370 Hom.: 32309 Cov.: 31

Gnomad AFR AF: 0.717

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.625

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

GnomAD4 genome AF: 0.649 AC: 98250 AN: 151490 Hom.: 32344 Cov.: 31 AF XY: 0.651 AC XY: 48189 AN XY: 73992

Gnomad4 AFR AF: 0.717

Gnomad4 AMR AF: 0.724

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.625

Alfa AF: 0.614 Hom.: 3437

Bravo AF: 0.663

Asia WGS AF: 0.753 AC: 2617 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	7.2
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225942; hg19: chr14-30525388;