rs1440983

chr14-30024055-G-A

Variant summary

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

The ENST00000549360.1(ENSG00000248975):n.85-43788C>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 0.0959 in 152,106 control chromosomes in the GnomAD database, including 1,318 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 0.096 (1318 hom., cov: 32)
• Consequence: ENST00000549360.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

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 (AFR) allele frequency at 95% confidence interval = 0.232 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.85-43788C>T		intron_variant, non_coding_transcript_variant		3
PRKD1	ENST00000549503.1	c.33+23655C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0957 AC: 14552 AN: 151990 Hom.: 1310 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0619

Gnomad ASJ AF: 0.0493

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0901

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0408

Gnomad OTH AF: 0.0889

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

GnomAD4 genome AF: 0.0959 AC: 14591 AN: 152106 Hom.: 1318 Cov.: 32 AF XY: 0.0945 AC XY: 7026 AN XY: 74364

Gnomad4 AFR AF: 0.236

Gnomad4 AMR AF: 0.0617

Gnomad4 ASJ AF: 0.0493

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0892

Gnomad4 FIN AF: 0.0132

Gnomad4 NFE AF: 0.0408

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.0914 Hom.: 187

Bravo AF: 0.106

Asia WGS AF: 0.0630 AC: 220 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	5.2
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440983; hg19: chr14-30493261;