chr2-218271478-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_015488.5(PNKD):c.165C>T(p.Pro55Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000434 in 1,614,178 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00026 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000021 ( 0 hom. )
Consequence
PNKD
NM_015488.5 synonymous
NM_015488.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.289
Publications
0 publications found
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 Gene-Disease associations (from GenCC):
- paroxysmal nonkinesigenic dyskinesia 1Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Orphanet
- Tourette syndromeInheritance: AD Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -17 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
Variant 2-218271478-C-T is Benign according to our data. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-218271478-C-T is described in CliVar as Likely_benign. Clinvar id is 415730.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=0.289 with no splicing effect.
BS2
High AC in GnomAd4 at 39 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNKD | NM_015488.5 | c.165C>T | p.Pro55Pro | synonymous_variant | Exon 2 of 10 | ENST00000273077.9 | NP_056303.3 | |
PNKD | NM_001077399.3 | c.165C>T | p.Pro55Pro | synonymous_variant | Exon 2 of 3 | NP_001070867.1 | ||
PNKD | XM_017003771.2 | c.165C>T | p.Pro55Pro | synonymous_variant | Exon 2 of 9 | XP_016859260.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152220Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
36
AN:
152220
Hom.:
Cov.:
33
Gnomad AFR
AF:
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Gnomad OTH
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GnomAD2 exomes AF: 0.0000358 AC: 9AN: 251468 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
AF:
AC:
9
AN:
251468
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.0000212 AC: 31AN: 1461840Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727234 show subpopulations
GnomAD4 exome
AF:
AC:
31
AN:
1461840
Hom.:
Cov.:
31
AF XY:
AC XY:
10
AN XY:
727234
show subpopulations
African (AFR)
AF:
AC:
24
AN:
33478
American (AMR)
AF:
AC:
4
AN:
44720
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
1
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53412
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1111978
Other (OTH)
AF:
AC:
2
AN:
60390
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.478
Heterozygous variant carriers
0
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4
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Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome AF: 0.000256 AC: 39AN: 152338Hom.: 0 Cov.: 33 AF XY: 0.000362 AC XY: 27AN XY: 74486 show subpopulations
GnomAD4 genome
AF:
AC:
39
AN:
152338
Hom.:
Cov.:
33
AF XY:
AC XY:
27
AN XY:
74486
show subpopulations
African (AFR)
AF:
AC:
28
AN:
41582
American (AMR)
AF:
AC:
11
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
0
AN:
4830
European-Finnish (FIN)
AF:
AC:
0
AN:
10618
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68034
Other (OTH)
AF:
AC:
0
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.496
Heterozygous variant carriers
0
2
4
6
8
10
0.00
0.20
0.40
0.60
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0.95
Allele balance
Age Distribution
Genome Het
Variant carriers
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Age
Alfa
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Paroxysmal nonkinesigenic dyskinesia Benign:1
Dec 02, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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