dbSNP rs116144189: PNKD:p.Arg313Arg (chr2-218344525-G-A) – ACMG Classification: Benign (-19 pts)

Variant summary

Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2

The NM_015488.5(PNKD):c.939G>A(p.Arg313Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.017 in 1,593,238 control chromosomes in the GnomAD database, including 287 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.013 ( 22 hom., cov: 32)

Exomes 𝑓: 0.017 ( 265 hom. )

Consequence

PNKD
NM_015488.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: 3.42

Publications

4 publications found

Variant links:

Genes affected

PNKD (HGNC:9153): (PNKD metallo-beta-lactamase domain containing) This gene is thought to play a role in the regulation of myofibrillogenesis. Mutations in this gene have been associated with the movement disorder paroxysmal non-kinesigenic dyskinesia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]

PNKD links:

CATIP-AS2 (HGNC:41079): (CATIP antisense RNA 2)

CATIP-AS2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -19 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.35).

BP6

Variant 2-218344525-G-A is Benign according to our data. Variant chr2-218344525-G-A is described in ClinVar as Benign. ClinVar VariationId is 334327.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=3.42 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0132 (2011/152312) while in subpopulation NFE AF = 0.0191 (1301/68022). AF 95% confidence interval is 0.0183. There are 22 homozygotes in GnomAd4. There are 955 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 2011 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015488.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PNKD	NM_015488.5	MANE Select	c.939G>A	p.Arg313Arg	synonymous	Exon 9 of 10	NP_056303.3
PNKD	NM_022572.4		c.867G>A	p.Arg289Arg	synonymous	Exon 8 of 9	NP_072094.1	Q8N490-3
CATIP-AS2	NR_125777.1		n.120+6635C>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
PNKD	ENST00000273077.9	TSL:1 MANE Select	c.939G>A	p.Arg313Arg	synonymous	Exon 9 of 10	ENSP00000273077.4	Q8N490-1
PNKD	ENST00000258362.7	TSL:1	c.867G>A	p.Arg289Arg	synonymous	Exon 8 of 9	ENSP00000258362.3	Q8N490-3
PNKD	ENST00000685415.1		c.1056G>A	p.Arg352Arg	synonymous	Exon 10 of 11	ENSP00000510415.1	A0A8I5KXK0

Frequencies

GnomAD3 genomes

AF:

0.0132

AC:

2011

AN:

152194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00401

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.0134

Gnomad ASJ

AF:

0.0262

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00496

Gnomad FIN

AF:

0.0166

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.0191

Gnomad OTH

AF:

0.0124

GnomAD2 exomes

AF:

0.0134

AC:

2868

AN:

213854

AF XY:

0.0135

show subpopulations

Gnomad AFR exome

AF:

0.00387

Gnomad AMR exome

AF:

0.0110

Gnomad ASJ exome

AF:

0.0244

Gnomad EAS exome

AF:

0.000188

Gnomad FIN exome

AF:

0.0183

Gnomad NFE exome

AF:

0.0179

Gnomad OTH exome

AF:

0.0169

GnomAD4 exome

AF:

0.0174

AC:

25093

AN:

1440926

Hom.:

265

Cov.:

AF XY:

0.0173

AC XY:

12358

AN XY:

714896

show subpopulations

African (AFR)

AF:

0.00275

AC:

AN:

33144

American (AMR)

AF:

0.0104

AC:

425

AN:

40886

Ashkenazi Jewish (ASJ)

AF:

0.0230

AC:

590

AN:

25650

East Asian (EAS)

AF:

0.000103

AC:

AN:

38818

South Asian (SAS)

AF:

0.00509

AC:

425

AN:

83460

European-Finnish (FIN)

AF:

0.0174

AC:

905

AN:

51896

Middle Eastern (MID)

AF:

0.0164

AC:

AN:

5740

European-Non Finnish (NFE)

AF:

0.0196

AC:

21589

AN:

1101720

Other (OTH)

AF:

0.0163

AC:

970

AN:

59612

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.485

Heterozygous variant carriers

1338

2676

4015

5353

6691

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

816

1632

2448

3264

4080

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0132

AC:

2011

AN:

152312

Hom.:

Cov.:

AF XY:

0.0128

AC XY:

955

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.00399

AC:

166

AN:

41562

American (AMR)

AF:

0.0134

AC:

205

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0262

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5186

South Asian (SAS)

AF:

0.00497

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.0166

AC:

176

AN:

10618

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0191

AC:

1301

AN:

68022

Other (OTH)

AF:

0.0123

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

188

283

377

471

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0173

Hom.:

Bravo

AF:

0.0120

Asia WGS

AF:

0.000866

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (4)

Paroxysmal nonkinesigenic dyskinesia (1)

Paroxysmal nonkinesigenic dyskinesia 1 (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.35

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

3.4

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over