NM_024675.4(PALB2):c.3351-150_*2del AND Malignant tumor of breast

Germline classification:: Likely pathogenic (1 submission)
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001354466.2

Allele description [Variation Report for NM_024675.4(PALB2):c.3351-150_*2del]

NM_024675.4(PALB2):c.3351-150_*2del

Gene:

PALB2:partner and localizer of BRCA2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

16p12.2

Genomic location:

Preferred name:

NM_024675.4(PALB2):c.3351-150_*2del

HGVS:

NC_000016.10:g.23603457_23603819del
NG_007406.1:g.42539_42901del
NM_024675.4:c.3351-150_*2delMANE SELECT
LRG_308:g.42539_42901del
NC_000016.9:g.23614778_23615140del

Links:

dbSNP: rs2142250624

NCBI 1000 Genomes Browser:

rs2142250624

Molecular consequence:

NM_024675.4:c.3351-150_*2del - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Name:: Malignant tumor of breast
Synonyms:: Malignant breast neoplasm; Cancer breast
Identifiers:: MONDO: MONDO:0007254; MedGen: C0006142

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001549091	Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR) See additional submitters Franklin by Genoox	no assertion criteria provided	Likely pathogenic	unknown	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001549091

Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria provided

Likely pathogenic

unknown

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001549091.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The PALB2 c.3202-?_3561+?del variant (chr:16 g.23614779_23619332del GRCh37) results in an in-frame deletion of exons 12-13, although the precise breakpoints of this deletion were not determined nor were the effects of this variant on the resulting mRNA or protein product determined. The variant was identified in a patient with breast and pancreas cancer (at ages 47 and 61 respectively) and whose mother died of pancreas cancer at age 83 (Tischkowitz 2009). The variant was not identified in dbSNP, ClinVar, LOVD 3.0, the Exome Aggregation Consortium (August 8th 2016) or the Genome Aggregation Database (Feb 27, 2017). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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