rs2413739
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001184970.3(PACSIN2):c.-78+13991G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 152,034 control chromosomes in the GnomAD database, including 14,360 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 0.43 ( 14360 hom., cov: 32)
Consequence
PACSIN2
NM_001184970.3 intron
NM_001184970.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0540
Genes affected
PACSIN2 (HGNC:8571): (protein kinase C and casein kinase substrate in neurons 2) This gene is a member of the protein kinase C and casein kinase substrate in neurons family. The encoded protein is involved in linking the actin cytoskeleton with vesicle formation by regulating tubulin polymerization. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
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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=-0.92).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PACSIN2 | NM_001184970.3 | c.-78+13991G>A | intron_variant | ENST00000263246.8 | |||
PACSIN2 | NM_001349969.2 | c.-78+13991G>A | intron_variant | ||||
PACSIN2 | NM_001349971.2 | c.-78+13991G>A | intron_variant | ||||
PACSIN2 | NM_001349974.2 | c.-64+13991G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PACSIN2 | ENST00000263246.8 | c.-78+13991G>A | intron_variant | 1 | NM_001184970.3 | A1 | |||
PACSIN2 | ENST00000422336.5 | c.-78+1280G>A | intron_variant | 5 | |||||
PACSIN2 | ENST00000453643.5 | c.-238-7250G>A | intron_variant | 5 | |||||
PACSIN2 | ENST00000445706.5 | n.78+13991G>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.426 AC: 64766AN: 151916Hom.: 14328 Cov.: 32
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.427 AC: 64844AN: 152034Hom.: 14360 Cov.: 32 AF XY: 0.420 AC XY: 31235AN XY: 74326
GnomAD4 genome
?
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31235
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74326
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1012
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3478
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
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at