7-83096302-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_033026.6(PCLO):​c.3300+37948C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.459 in 151,790 control chromosomes in the GnomAD database, including 16,418 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 0.46 ( 16418 hom., cov: 31)

Consequence

PCLO
NM_033026.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.386
Variant links:
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PCLONM_033026.6 linkuse as main transcriptc.3300+37948C>G intron_variant ENST00000333891.14 NP_149015.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PCLOENST00000333891.14 linkuse as main transcriptc.3300+37948C>G intron_variant 2 NM_033026.6 ENSP00000334319.8 Q9Y6V0-5
PCLOENST00000423517.6 linkuse as main transcriptc.3300+37948C>G intron_variant 5 ENSP00000388393.2 Q9Y6V0-6
PCLOENST00000461143.1 linkuse as main transcriptn.361+37948C>G intron_variant 2

Frequencies

GnomAD3 genomes
AF:
0.459
AC:
69635
AN:
151672
Hom.:
16394
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.479
Gnomad AMI
AF:
0.371
Gnomad AMR
AF:
0.541
Gnomad ASJ
AF:
0.387
Gnomad EAS
AF:
0.712
Gnomad SAS
AF:
0.408
Gnomad FIN
AF:
0.517
Gnomad MID
AF:
0.346
Gnomad NFE
AF:
0.409
Gnomad OTH
AF:
0.479
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.459
AC:
69711
AN:
151790
Hom.:
16418
Cov.:
31
AF XY:
0.467
AC XY:
34601
AN XY:
74148
show subpopulations
Gnomad4 AFR
AF:
0.479
Gnomad4 AMR
AF:
0.542
Gnomad4 ASJ
AF:
0.387
Gnomad4 EAS
AF:
0.712
Gnomad4 SAS
AF:
0.407
Gnomad4 FIN
AF:
0.517
Gnomad4 NFE
AF:
0.409
Gnomad4 OTH
AF:
0.484
Alfa
AF:
0.272
Hom.:
612
Bravo
AF:
0.466
Asia WGS
AF:
0.586
AC:
2037
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
0.60
DANN
Benign
0.76

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: rs6947662; hg19: chr7-82725618; API