rs7792042

Variant names:

• chr7-82855427-G-A
• rs7792042
• NM_033026.6:c.13655-8180C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-82855427-G-A
• chr7-82855427-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_033026.6(PCLO):​c.13655-8180C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,958 control chromosomes in the GnomAD database, including 5,368 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 0.26 (5368 hom., cov: 32)
• Consequence: PCLO NM_033026.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.244
• Publications: 2 publications found

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]

PCLO Gene-Disease associations (from GenCC):

• pontocerebellar hypoplasia type 3

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PCLO	NM_033026.6	c.13655-8180C>T		intron_variant	Intron 10 of 24	ENST00000333891.14	NP_149015.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PCLO	ENST00000333891.14	c.13655-8180C>T		intron_variant	Intron 10 of 24	2	NM_033026.6	ENSP00000334319.8

Frequencies

GnomAD3 genomes AF: 0.258 AC: 39123 AN: 151840 Hom.: 5359 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.338

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.248

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.258 AC: 39158 AN: 151958 Hom.: 5368 Cov.: 32 AF XY: 0.260 AC XY: 19286 AN XY: 74268

African (AFR) AF: 0.192 AC: 7983 AN: 41472

American (AMR) AF: 0.223 AC: 3404 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 919 AN: 3468

East Asian (EAS) AF: 0.286 AC: 1481 AN: 5170

South Asian (SAS) AF: 0.257 AC: 1240 AN: 4824

European-Finnish (FIN) AF: 0.338 AC: 3562 AN: 10526

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.292 AC: 19818 AN: 67942

Other (OTH) AF: 0.246 AC: 519 AN: 2110

Alfa AF: 0.261 Hom.: 702

Bravo AF: 0.244

Asia WGS AF: 0.241 AC: 837 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.3
DANN	Benign	0.58
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7792042; hg19: chr7-82484743;