Variant X-153672995-G-A 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_001366977.1(PNCK):c.68+14C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 1,168,100 control chromosomes in the GnomAD database, including 5,486 homozygotes. There are 42,955 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.099 ( 457 hom., 2791 hem., cov: 22)

Exomes 𝑓: 0.12 ( 5029 hom. 40164 hem. )

Consequence

PNCK
NM_001366977.1 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.207

Variant links:

Genes affected

PNCK (HGNC:13415): (pregnancy up-regulated nonubiquitous CaM kinase) PNCK is a member of the calcium/calmodulin-dependent protein kinase family of protein serine/threonine kinases (see CAMK1; MIM 604998) (Gardner et al., 2000 [PubMed 10673339]).[supplied by OMIM, Mar 2008]

PNCK links:

PNCK (HGNC:):

PNCK links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant X-153672995-G-A is Benign according to our data. Variant chrX-153672995-G-A is described in ClinVar as [Benign]. Clinvar id is 1247495.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PNCK	NM_001366977.1 linkuse as main transcript	c.68+14C>T		intron_variant		ENST00000340888.8	NP_001353906.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PNCK	ENST00000340888.8 linkuse as main transcript	c.68+14C>T		intron_variant		5	NM_001366977.1	ENSP00000340586.4		Q6P2M8-1

Frequencies

GnomAD3 genomes

AF:

0.0990

AC:

10687

AN:

107967

Hom.:

457

Cov.:

AF XY:

0.0903

AC XY:

2783

AN XY:

30833

show subpopulations

Gnomad AFR

AF:

0.0867

Gnomad AMI

AF:

0.0382

Gnomad AMR

AF:

0.0674

Gnomad ASJ

AF:

0.0548

Gnomad EAS

AF:

0.0860

Gnomad SAS

AF:

0.151

Gnomad FIN

AF:

0.0849

Gnomad MID

AF:

0.0844

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.0957

GnomAD3 exomes

AF:

0.101

AC:

13043

AN:

129421

Hom.:

515

AF XY:

0.106

AC XY:

4125

AN XY:

38907

show subpopulations

Gnomad AFR exome

AF:

0.0860

Gnomad AMR exome

AF:

0.0644

Gnomad ASJ exome

AF:

0.0604

Gnomad EAS exome

AF:

0.0841

Gnomad SAS exome

AF:

0.150

Gnomad FIN exome

AF:

0.0960

Gnomad NFE exome

AF:

0.114

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

AF:

0.116

AC:

123188

AN:

1060083

Hom.:

5029

Cov.:

AF XY:

0.118

AC XY:

40164

AN XY:

341131

show subpopulations

Gnomad4 AFR exome

AF:

0.0901

Gnomad4 AMR exome

AF:

0.0646

Gnomad4 ASJ exome

AF:

0.0599

Gnomad4 EAS exome

AF:

0.115

Gnomad4 SAS exome

AF:

0.153

Gnomad4 FIN exome

AF:

0.105

Gnomad4 NFE exome

AF:

0.119

Gnomad4 OTH exome

AF:

0.107

GnomAD4 genome

AF:

0.0990

AC:

10690

AN:

108017

Hom.:

457

Cov.:

AF XY:

0.0903

AC XY:

2791

AN XY:

30893

show subpopulations

Gnomad4 AFR

AF:

0.0868

Gnomad4 AMR

AF:

0.0673

Gnomad4 ASJ

AF:

0.0548

Gnomad4 EAS

AF:

0.0863

Gnomad4 SAS

AF:

0.152

Gnomad4 FIN

AF:

0.0849

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.0951

Alfa

AF:

0.101

Hom.:

838

Bravo

AF:

0.0979

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 01, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.74

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.15

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