Variant 14-29578374-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002742.3(PRKD1):c.2435-14G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 1,583,670 control chromosomes in the GnomAD database, including 426,890 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.71 ( 38593 hom., cov: 28)

Exomes 𝑓: 0.73 ( 388297 hom. )

Consequence

PRKD1
NM_002742.3 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 2.26

Variant links:

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]

PRKD1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 14-29578374-C-T is Benign according to our data. Variant chr14-29578374-C-T is described in ClinVar as [Benign]. Clinvar id is 1327445.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRKD1	NM_002742.3 linkuse as main transcript	c.2435-14G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000331968.11	NP_002733.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRKD1	ENST00000331968.11 linkuse as main transcript	c.2435-14G>A		splice_polypyrimidine_tract_variant, intron_variant		1	NM_002742.3	ENSP00000333568	P3

Frequencies

GnomAD3 genomes

AF:

0.712

AC:

107725

AN:

151264

Hom.:

38558

Cov.:

show subpopulations

Gnomad AFR

AF:

0.723

Gnomad AMI

AF:

0.758

Gnomad AMR

AF:

0.669

Gnomad ASJ

AF:

0.670

Gnomad EAS

AF:

0.568

Gnomad SAS

AF:

0.557

Gnomad FIN

AF:

0.647

Gnomad MID

AF:

0.649

Gnomad NFE

AF:

0.749

Gnomad OTH

AF:

0.694

GnomAD3 exomes

AF:

0.682

AC:

165152

AN:

242046

Hom.:

57073

AF XY:

0.680

AC XY:

89174

AN XY:

131096

show subpopulations

Gnomad AFR exome

AF:

0.720

Gnomad AMR exome

AF:

0.646

Gnomad ASJ exome

AF:

0.660

Gnomad EAS exome

AF:

0.554

Gnomad SAS exome

AF:

0.567

Gnomad FIN exome

AF:

0.653

Gnomad NFE exome

AF:

0.747

Gnomad OTH exome

AF:

0.680

GnomAD4 exome

AF:

0.733

AC:

1049820

AN:

1432288

Hom.:

388297

Cov.:

AF XY:

0.728

AC XY:

519537

AN XY:

713356

show subpopulations

Gnomad4 AFR exome

AF:

0.721

Gnomad4 AMR exome

AF:

0.646

Gnomad4 ASJ exome

AF:

0.668

Gnomad4 EAS exome

AF:

0.572

Gnomad4 SAS exome

AF:

0.575

Gnomad4 FIN exome

AF:

0.652

Gnomad4 NFE exome

AF:

0.762

Gnomad4 OTH exome

AF:

0.709

GnomAD4 genome

AF:

0.712

AC:

107816

AN:

151382

Hom.:

38593

Cov.:

AF XY:

0.704

AC XY:

52036

AN XY:

73964

show subpopulations

Gnomad4 AFR

AF:

0.723

Gnomad4 AMR

AF:

0.669

Gnomad4 ASJ

AF:

0.670

Gnomad4 EAS

AF:

0.569

Gnomad4 SAS

AF:

0.558

Gnomad4 FIN

AF:

0.647

Gnomad4 NFE

AF:

0.749

Gnomad4 OTH

AF:

0.696

Alfa

AF:

0.719

Hom.:

7883

Bravo

AF:

0.714

Asia WGS

AF:

0.570

AC:

1979

AN:

3462

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Congenital heart defects and ectodermal dysplasia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Oct 25, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

DANN

Benign

0.52

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over