Variant chr19-49861087-G-GC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The ENST00000636840.1(PNKP):c.59+520_59+521insG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0378 in 677,362 control chromosomes in the GnomAD database, including 914 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.026 ( 93 hom., cov: 32)

Exomes 𝑓: 0.041 ( 821 hom. )

Consequence

PNKP
ENST00000636840.1 intron

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.500

Variant links:

Genes affected

PNKP (HGNC:9154): (polynucleotide kinase 3'-phosphatase) This locus represents a gene involved in DNA repair. In response to ionizing radiation or oxidative damage, the protein encoded by this locus catalyzes 5' phosphorylation and 3' dephosphorylation of nucleic acids. Mutations at this locus have been associated with microcephaly, seizures, and developmental delay.[provided by RefSeq, Sep 2010]

PNKP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 19-49861087-G-GC is Benign according to our data. Variant chr19-49861087-G-GC is described in ClinVar as [Likely_benign]. Clinvar id is 1208797.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PNKP	ENST00000636840.1 linkuse as main transcript	c.59+520_59+521insG		intron_variant		5		ENSP00000490737

Frequencies

GnomAD3 genomes

AF:

0.0262

AC:

3988

AN:

152154

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00678

Gnomad AMI

AF:

0.0650

Gnomad AMR

AF:

0.0181

Gnomad ASJ

AF:

0.0441

Gnomad EAS

AF:

0.0591

Gnomad SAS

AF:

0.121

Gnomad FIN

AF:

0.0192

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0301

Gnomad OTH

AF:

0.0282

GnomAD4 exome

AF:

0.0412

AC:

21635

AN:

525090

Hom.:

821

AF XY:

0.0453

AC XY:

12819

AN XY:

282670

show subpopulations

Gnomad4 AFR exome

AF:

0.00748

Gnomad4 AMR exome

AF:

0.0118

Gnomad4 ASJ exome

AF:

0.0435

Gnomad4 EAS exome

AF:

0.0727

Gnomad4 SAS exome

AF:

0.117

Gnomad4 FIN exome

AF:

0.0233

Gnomad4 NFE exome

AF:

0.0312

Gnomad4 OTH exome

AF:

0.0353

GnomAD4 genome

AF:

0.0262

AC:

3996

AN:

152272

Hom.:

Cov.:

AF XY:

0.0265

AC XY:

1974

AN XY:

74450

show subpopulations

Gnomad4 AFR

AF:

0.00676

Gnomad4 AMR

AF:

0.0181

Gnomad4 ASJ

AF:

0.0441

Gnomad4 EAS

AF:

0.0592

Gnomad4 SAS

AF:

0.121

Gnomad4 FIN

AF:

0.0192

Gnomad4 NFE

AF:

0.0301

Gnomad4 OTH

AF:

0.0322

Alfa

AF:

0.0239

Hom.:

Bravo

AF:

0.0230

Asia WGS

AF:

0.122

AC:

422

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 14, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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