Variant rs1044305 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_138370.3(PKDCC):c.*56T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 1,505,726 control chromosomes in the GnomAD database, including 26,600 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 0.20 ( 3843 hom., cov: 33)

Exomes 𝑓: 0.16 ( 22757 hom. )

Consequence

PKDCC
NM_138370.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.925

Variant links:

Genes affected

PKDCC (HGNC:25123): (protein kinase domain containing, cytoplasmic) Enables non-membrane spanning protein tyrosine kinase activity. Involved in peptidyl-tyrosine phosphorylation and skeletal system development. Located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

PKDCC links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PKDCC	NM_138370.3 linkuse as main transcript	c.*56T>C		3_prime_UTR_variant	7/7	ENST00000294964.6	NP_612379.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PKDCC	ENST00000294964.6 linkuse as main transcript	c.*56T>C		3_prime_UTR_variant	7/7	1	NM_138370.3	ENSP00000294964	P1

Frequencies

GnomAD3 genomes

AF:

0.197

AC:

30019

AN:

152076

Hom.:

3827

Cov.:

show subpopulations

Gnomad AFR

AF:

0.265

Gnomad AMI

AF:

0.0625

Gnomad AMR

AF:

0.352

Gnomad ASJ

AF:

0.0772

Gnomad EAS

AF:

0.448

Gnomad SAS

AF:

0.204

Gnomad FIN

AF:

0.0718

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.188

GnomAD4 exome

AF:

0.161

AC:

217431

AN:

1353532

Hom.:

22757

Cov.:

AF XY:

0.159

AC XY:

107549

AN XY:

676040

show subpopulations

Gnomad4 AFR exome

AF:

0.271

Gnomad4 AMR exome

AF:

0.490

Gnomad4 ASJ exome

AF:

0.0797

Gnomad4 EAS exome

AF:

0.457

Gnomad4 SAS exome

AF:

0.195

Gnomad4 FIN exome

AF:

0.0790

Gnomad4 NFE exome

AF:

0.136

Gnomad4 OTH exome

AF:

0.164

GnomAD4 genome

AF:

0.198

AC:

30091

AN:

152194

Hom.:

3843

Cov.:

AF XY:

0.199

AC XY:

14801

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.265

Gnomad4 AMR

AF:

0.353

Gnomad4 ASJ

AF:

0.0772

Gnomad4 EAS

AF:

0.449

Gnomad4 SAS

AF:

0.205

Gnomad4 FIN

AF:

0.0718

Gnomad4 NFE

AF:

0.131

Gnomad4 OTH

AF:

0.191

Alfa

AF:

0.149

Hom.:

2179

Bravo

AF:

0.228

Asia WGS

AF:

0.307

AC:

1067

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.6

DANN

Benign

0.72

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over