chr2-218337761-G-A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015488.5(PNKD):​c.237-2022G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,058 control chromosomes in the GnomAD database, including 3,035 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 ( 3035 hom., cov: 31)

Consequence

PNKD
NM_015488.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.892

Publications

13 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]
CATIP-AS2 (HGNC:41079): (CATIP antisense RNA 2)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.01).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PNKDNM_015488.5 linkc.237-2022G>A intron_variant Intron 2 of 9 ENST00000273077.9 NP_056303.3 Q8N490-1A0A024R415

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PNKDENST00000273077.9 linkc.237-2022G>A intron_variant Intron 2 of 9 1 NM_015488.5 ENSP00000273077.4 Q8N490-1

Frequencies

GnomAD3 genomes
AF:
0.195
AC:
29646
AN:
151940
Hom.:
3038
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.179
Gnomad AMI
AF:
0.268
Gnomad AMR
AF:
0.251
Gnomad ASJ
AF:
0.220
Gnomad EAS
AF:
0.120
Gnomad SAS
AF:
0.0906
Gnomad FIN
AF:
0.137
Gnomad MID
AF:
0.351
Gnomad NFE
AF:
0.210
Gnomad OTH
AF:
0.226
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.195
AC:
29652
AN:
152058
Hom.:
3035
Cov.:
31
AF XY:
0.192
AC XY:
14239
AN XY:
74326
show subpopulations
African (AFR)
AF:
0.179
AC:
7419
AN:
41452
American (AMR)
AF:
0.251
AC:
3827
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.220
AC:
763
AN:
3470
East Asian (EAS)
AF:
0.121
AC:
624
AN:
5170
South Asian (SAS)
AF:
0.0903
AC:
435
AN:
4818
European-Finnish (FIN)
AF:
0.137
AC:
1451
AN:
10582
Middle Eastern (MID)
AF:
0.347
AC:
102
AN:
294
European-Non Finnish (NFE)
AF:
0.210
AC:
14307
AN:
67994
Other (OTH)
AF:
0.228
AC:
480
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1251
2502
3752
5003
6254
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
306
612
918
1224
1530
<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:
0.212
Hom.:
6944
Bravo
AF:
0.207
Asia WGS
AF:
0.102
AC:
355
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
0.96
DANN
Benign
0.61
PhyloP100
-0.89
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs12471773; hg19: chr2-219202484; API