2-218270471-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000248451.7(PNKD):c.-65G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000159 in 661,230 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000092 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00018 ( 0 hom. )
Consequence
PNKD
ENST00000248451.7 5_prime_UTR
ENST00000248451.7 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 2.61
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.21).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PNKD | NM_015488.5 | upstream_gene_variant | ENST00000273077.9 | NP_056303.3 | ||||
PNKD | NM_001077399.3 | upstream_gene_variant | NP_001070867.1 | |||||
PNKD | XM_017003771.2 | upstream_gene_variant | XP_016859260.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PNKD | ENST00000273077.9 | upstream_gene_variant | 1 | NM_015488.5 | ENSP00000273077 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152254Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000179 AC: 91AN: 508858Hom.: 0 Cov.: 7 AF XY: 0.000236 AC XY: 61AN XY: 258846
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GnomAD4 genome AF: 0.0000919 AC: 14AN: 152372Hom.: 0 Cov.: 33 AF XY: 0.000148 AC XY: 11AN XY: 74512
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Paroxysmal nonkinesigenic dyskinesia 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at