chr3-64354961-A-C
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000295902.11(PRICKLE2):c.128+89522T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,194 control chromosomes in the GnomAD database, including 2,542 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 0.18 ( 2542 hom., cov: 32)
Consequence
PRICKLE2
ENST00000295902.11 intron
ENST00000295902.11 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.07
Genes affected
PRICKLE2 (HGNC:20340): (prickle planar cell polarity protein 2) This gene encodes a homolog of Drosophila prickle. The exact function of this gene is not known, however, studies in mice suggest that it may be involved in seizure prevention. Mutations in this gene are associated with progressive myoclonic epilepsy type 5. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.74).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
use as main transcript | n.64354961A>C | intergenic_region |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRICKLE2 | ENST00000295902.11 | c.128+89522T>G | intron_variant | 5 | ENSP00000295902.7 | |||||
PRICKLE2 | ENST00000498162.2 | c.107+89522T>G | intron_variant | 5 | ENSP00000419951.2 | |||||
PRICKLE2 | ENST00000485770.2 | n.340+89522T>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.182 AC: 27620AN: 152076Hom.: 2537 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.182 AC: 27656AN: 152194Hom.: 2542 Cov.: 32 AF XY: 0.182 AC XY: 13539AN XY: 74410
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at