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Variant: NM_024675.3(PALB2):c.721A>G (p.Asn241Asp)

CA151529

126765 (ClinVar)

Gene: PALB2
Condition: hereditary breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: f1d80ff5-d93c-41ed-8272-b137d5131076
Approved on: 2023-04-05
Published on: 2023-04-07

HGVS expressions

NM_024675.3:c.721A>G
NM_024675.3(PALB2):c.721A>G (p.Asn241Asp)
NC_000016.10:g.23635825T>C
CM000678.2:g.23635825T>C
NC_000016.9:g.23647146T>C
CM000678.1:g.23647146T>C
NC_000016.8:g.23554647T>C
NG_007406.1:g.10533A>G
ENST00000261584.9:c.721A>G
ENST00000261584.8:c.721A>G
ENST00000565038.1:n.86+2025A>G
ENST00000568219.5:c.-165A>G
NM_024675.4:c.721A>G
NM_024675.4(PALB2):c.721A>G (p.Asn241Asp)
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Benign

Met criteria codes 4
BS2 BP1 BP2_Strong BA1
Not Met criteria codes 2
BS1 PM2

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PALB2 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hereditary Breast, Ovarian and Pancreatic Cancer VCEP
The c.721A>G variant in PALB2 is a missense variant predicted to predicted to cause substitution of asparagine by aspartic acid at amino acid 241 (p.Asn241Asp). This variant has been observed in three homozygous individuals with no features of FANCN, a condition with full penetrance at an early age (Ambry Genetics). The highest population minor filtering allele frequency in gnomAD v2.1.1 is 0.005509 in the African population, which is higher than the HBOP VCEP threshold (>0.001) for BA1, and therefore meets this criterion. PALB2, in which the variant was identified, is defined by the HBOP VCEP as a gene for which primarily truncating variants are known to cause disease. In summary, this variant meets the criteria to be classified as benign for autosomal dominant hereditary breast and pancreatic cancer and autosomal recessive FANCN based on the ACMG/AMP criteria applied, as specified by the HBOP VCEP (BA1, BS2, BP1)
Met criteria codes
BS2
This variant has been observed in a homozygous and/or compound heterozygous state (confirmed) in multiple individuals without Fanconi-Anemia (Ambry Genetics). (BS2_strong) (4 pts)
BP1
PALB2, in which the variant was identified, is defined by the HBOP VCEP as a gene for which primarily truncating variants are known to cause disease (BP1)
BP2_Strong
The c.721A>G (p.Asn241Asp) variant has been observed in more than four homozygous individuals with no features of Fanconi anemia subtype N, a condition with full penetrance at an early age (BP2_Stand-alone).
BA1
The highest population minor filtering allele frequency in gnomAD v2.1.1 is 0.005509 in the African population, which is higher than the HBOP VCEP threshold (>0.001) for BA1, and therefore meets this criterion (BA1).
Not Met criteria codes
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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