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2-218270205-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000691799.1(PNKD):n.70+485A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 1,476,054 control chromosomes in the GnomAD database, including 122,563 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.43 ( 14391 hom., cov: 34)
Exomes 𝑓: 0.40 ( 108172 hom. )

Consequence

PNKD
ENST00000691799.1 intron, non_coding_transcript

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.525
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]
AAMP (HGNC:18): (angio associated migratory cell protein) The gene is a member of the immunoglobulin superfamily. The encoded protein is associated with angiogenesis, with potential roles in endothelial tube formation and the migration of endothelial cells. It may also regulate smooth muscle cell migration via the RhoA pathway. The encoded protein can bind to heparin and may mediate heparin-sensitive cell adhesion. [provided by RefSeq, Oct 2014]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.69).
BP6
Variant 2-218270205-A-G is Benign according to our data. Variant chr2-218270205-A-G is described in ClinVar as [Benign]. Clinvar id is 1226098.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.505 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PNKDENST00000691799.1 linkuse as main transcriptn.70+485A>G intron_variant, non_coding_transcript_variant
AAMPENST00000444053.5 linkuse as main transcript upstream_gene_variant 1 P4

Frequencies

GnomAD3 genomes
AF:
0.431
AC:
65507
AN:
152048
Hom.:
14386
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.511
Gnomad AMI
AF:
0.429
Gnomad AMR
AF:
0.464
Gnomad ASJ
AF:
0.393
Gnomad EAS
AF:
0.396
Gnomad SAS
AF:
0.356
Gnomad FIN
AF:
0.290
Gnomad MID
AF:
0.519
Gnomad NFE
AF:
0.405
Gnomad OTH
AF:
0.453
GnomAD4 exome
AF:
0.403
AC:
533569
AN:
1323888
Hom.:
108172
Cov.:
20
AF XY:
0.401
AC XY:
262177
AN XY:
653034
show subpopulations
Gnomad4 AFR exome
AF:
0.516
Gnomad4 AMR exome
AF:
0.464
Gnomad4 ASJ exome
AF:
0.391
Gnomad4 EAS exome
AF:
0.389
Gnomad4 SAS exome
AF:
0.354
Gnomad4 FIN exome
AF:
0.305
Gnomad4 NFE exome
AF:
0.406
Gnomad4 OTH exome
AF:
0.412
GnomAD4 genome
AF:
0.431
AC:
65542
AN:
152166
Hom.:
14391
Cov.:
34
AF XY:
0.427
AC XY:
31806
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.511
Gnomad4 AMR
AF:
0.463
Gnomad4 ASJ
AF:
0.393
Gnomad4 EAS
AF:
0.395
Gnomad4 SAS
AF:
0.357
Gnomad4 FIN
AF:
0.290
Gnomad4 NFE
AF:
0.405
Gnomad4 OTH
AF:
0.451
Alfa
AF:
0.421
Hom.:
4242
Bravo
AF:
0.448
Asia WGS
AF:
0.339
AC:
1176
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxJul 05, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.69
Cadd
Benign
6.7
Dann
Benign
0.73

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1877714; hg19: chr2-219134928; COSMIC: COSV50307941; COSMIC: COSV50307941; API