NM_007166.4:c.1840-241A>C

Variant names:

• chr11-85975053-T-G
• rs532470
• NM_007166.4:c.1840-241A>C

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_007166.4(PICALM):​c.1840-241A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.444 in 151,982 control chromosomes in the GnomAD database, including 15,205 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.44 (15205 hom., cov: 32)
• Consequence: PICALM NM_007166.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.153
• Publications: 10 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BP6: Variant 11-85975053-T-G is Benign according to our data. Variant chr11-85975053-T-G is described in ClinVar as Benign. ClinVar VariationId is 1261860.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007166.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PICALM	NM_007166.4	MANE Select	c.1840-241A>C		intron	N/A	NP_009097.2
	PICALM	NM_001206946.2		c.1819-241A>C		intron	N/A	NP_001193875.1
	PICALM	NM_001411034.1		c.1780-241A>C		intron	N/A	NP_001397963.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PICALM	ENST00000393346.8	TSL:1 MANE Select	c.1840-241A>C		intron	N/A	ENSP00000377015.3
	PICALM	ENST00000526033.5	TSL:1	c.1819-241A>C		intron	N/A	ENSP00000433846.1
	PICALM	ENST00000532317.5	TSL:1	c.1714-241A>C		intron	N/A	ENSP00000436958.1

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67487 AN: 151864 Hom.: 15202 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.444 AC: 67518 AN: 151982 Hom.: 15205 Cov.: 32 AF XY: 0.439 AC XY: 32628 AN XY: 74284

African (AFR) AF: 0.468 AC: 19378 AN: 41448

American (AMR) AF: 0.452 AC: 6891 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.401 AC: 1392 AN: 3472

East Asian (EAS) AF: 0.594 AC: 3067 AN: 5160

South Asian (SAS) AF: 0.512 AC: 2466 AN: 4812

European-Finnish (FIN) AF: 0.301 AC: 3180 AN: 10564

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.437 AC: 29715 AN: 67956

Other (OTH) AF: 0.439 AC: 925 AN: 2106

Alfa AF: 0.376 Hom.: 1856

Bravo AF: 0.454

Asia WGS AF: 0.511 AC: 1777 AN: 3474

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 12, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.5
DANN	Benign	0.83
PhyloP100		0.15
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: rs532470; hg19: chr11-85686096;