Variant X-153670532-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2

The NM_001366977.1(PNCK):c.957C>T(p.Gly319Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00662 in 1,209,258 control chromosomes in the GnomAD database, including 23 homozygotes. There are 2,478 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0051 ( 1 hom., 151 hem., cov: 25)

Exomes 𝑓: 0.0068 ( 22 hom. 2327 hem. )

Consequence

PNCK
NM_001366977.1 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.94

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 -12 ACMG points.

BP6

Variant X-153670532-G-A is Benign according to our data. Variant chrX-153670532-G-A is described in ClinVar as [Benign]. Clinvar id is 782180.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Hemizygotes in GnomAd4 at 151 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PNCK	NM_001366977.1 linkuse as main transcript	c.957C>T	p.Gly319Gly	synonymous_variant	11/12	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.957C>T	p.Gly319Gly	synonymous_variant	11/12	5	NM_001366977.1	ENSP00000340586.4		Q6P2M8-1

Frequencies

GnomAD3 genomes

AF:

0.00510

AC:

577

AN:

113097

Hom.:

Cov.:

AF XY:

0.00428

AC XY:

151

AN XY:

35247

show subpopulations

Gnomad AFR

AF:

0.00103

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00185

Gnomad ASJ

AF:

0.00525

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000719

Gnomad FIN

AF:

0.000944

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00937

Gnomad OTH

AF:

0.00261

GnomAD3 exomes

AF:

0.00431

AC:

756

AN:

175469

Hom.:

AF XY:

0.00457

AC XY:

285

AN XY:

62389

show subpopulations

Gnomad AFR exome

AF:

0.000648

Gnomad AMR exome

AF:

0.00159

Gnomad ASJ exome

AF:

0.00358

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00185

Gnomad FIN exome

AF:

0.00297

Gnomad NFE exome

AF:

0.00745

Gnomad OTH exome

AF:

0.00529

GnomAD4 exome

AF:

0.00678

AC:

7429

AN:

1096111

Hom.:

Cov.:

AF XY:

0.00643

AC XY:

2327

AN XY:

362099

show subpopulations

Gnomad4 AFR exome

AF:

0.000834

Gnomad4 AMR exome

AF:

0.00177

Gnomad4 ASJ exome

AF:

0.00362

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00178

Gnomad4 FIN exome

AF:

0.00349

Gnomad4 NFE exome

AF:

0.00810

Gnomad4 OTH exome

AF:

0.00479

GnomAD4 genome

AF:

0.00510

AC:

577

AN:

113147

Hom.:

Cov.:

AF XY:

0.00428

AC XY:

151

AN XY:

35307

show subpopulations

Gnomad4 AFR

AF:

0.00102

Gnomad4 AMR

AF:

0.00184

Gnomad4 ASJ

AF:

0.00525

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000721

Gnomad4 FIN

AF:

0.000944

Gnomad4 NFE

AF:

0.00938

Gnomad4 OTH

AF:

0.00258

Alfa

AF:

0.00702

Hom.:

Bravo

AF:

0.00432

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	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 22, 2018	- -
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

9.1

DANN

Benign

0.86

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.70

Details are displayed if max score is > 0.2

DS_DG_spliceai

0.70

Position offset: 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