rs10792820

Variant summary

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

The ENST00000393346.8(PICALM):​c.1259-2532T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.211 in 152,146 control chromosomes in the GnomAD database, including 3,812 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 0.21 ( 3812 hom., cov: 32)

Consequence

PICALM
ENST00000393346.8 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0560
Variant links:
Genes affected
PICALM (HGNC:15514): (phosphatidylinositol binding clathrin assembly protein) This gene encodes a clathrin assembly protein, which recruits clathrin and adaptor protein complex 2 (AP2) to cell membranes at sites of coated-pit formation and clathrin-vesicle assembly. The protein may be required to determine the amount of membrane to be recycled, possibly by regulating the size of the clathrin cage. The protein is involved in AP2-dependent clathrin-mediated endocytosis at the neuromuscular junction. A chromosomal translocation t(10;11)(p13;q14) leading to the fusion of this gene and the MLLT10 gene is found in acute lymphoblastic leukemia, acute myeloid leukemia and malignant lymphomas. The polymorphisms of this gene are associated with the risk of Alzheimer disease. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PICALMNM_007166.4 linkuse as main transcriptc.1259-2532T>G intron_variant ENST00000393346.8 NP_009097.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PICALMENST00000393346.8 linkuse as main transcriptc.1259-2532T>G intron_variant 1 NM_007166.4 ENSP00000377015 Q13492-1

Frequencies

GnomAD3 genomes
AF:
0.211
AC:
32053
AN:
152028
Hom.:
3811
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.114
Gnomad AMI
AF:
0.139
Gnomad AMR
AF:
0.237
Gnomad ASJ
AF:
0.201
Gnomad EAS
AF:
0.482
Gnomad SAS
AF:
0.315
Gnomad FIN
AF:
0.175
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.243
Gnomad OTH
AF:
0.215
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.211
AC:
32064
AN:
152146
Hom.:
3812
Cov.:
32
AF XY:
0.210
AC XY:
15617
AN XY:
74378
show subpopulations
Gnomad4 AFR
AF:
0.113
Gnomad4 AMR
AF:
0.237
Gnomad4 ASJ
AF:
0.201
Gnomad4 EAS
AF:
0.482
Gnomad4 SAS
AF:
0.317
Gnomad4 FIN
AF:
0.175
Gnomad4 NFE
AF:
0.243
Gnomad4 OTH
AF:
0.218
Alfa
AF:
0.241
Hom.:
8589
Bravo
AF:
0.209
Asia WGS
AF:
0.360
AC:
1248
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
2.0
DANN
Benign
0.51

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: rs10792820; hg19: chr11-85703974; API