chr7-82758730-CA-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_033026.6(PCLO):c.15289-16del variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000758 in 1,318,954 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.6e-7 ( 0 hom. )
Consequence
PCLO
NM_033026.6 splice_polypyrimidine_tract, intron
NM_033026.6 splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.70
Genes affected
PCLO (HGNC:13406): (piccolo presynaptic cytomatrix protein) The protein encoded by this gene is part of the presynaptic cytoskeletal matrix, which is involved in establishing active synaptic zones and in synaptic vesicle trafficking. Variations in this gene have been associated with bipolar disorder and major depressive disorder. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]
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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;
BP6
?
Variant 7-82758730-CA-C is Benign according to our data. Variant chr7-82758730-CA-C is described in ClinVar as [Benign]. Clinvar id is 1994695.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCLO | NM_033026.6 | c.15289-16del | splice_polypyrimidine_tract_variant, intron_variant | ENST00000333891.14 | |||
PCLO | XM_017012006.3 | c.8377-16del | splice_polypyrimidine_tract_variant, intron_variant | ||||
PCLO | XM_047420210.1 | c.15472-16del | splice_polypyrimidine_tract_variant, intron_variant | ||||
PCLO | XM_047420211.1 | c.14998-16del | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCLO | ENST00000333891.14 | c.15289-16del | splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_033026.6 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 7.58e-7 AC: 1AN: 1318954Hom.: 0 Cov.: 20 AF XY: 0.00 AC XY: 0AN XY: 663858
GnomAD4 exome
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1
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1318954
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20
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0
AN XY:
663858
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
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 submitter | clinical testing | Invitae | May 16, 2022 | - - |
Computational scores
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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
Publications
No publications associated with this variant yet.