The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_024675.4(PALB2):c.212-33A>C

CA269519

126634 (ClinVar)

Gene: PALB2
Condition: hereditary breast cancer
Inheritance Mode: Autosomal dominant inheritance
UUID: 6c7f2dd8-478c-4c7a-8a3c-4278300dc575
Approved on: 2023-06-15
Published on: 2023-06-15

HGVS expressions

NM_024675.4:c.212-33A>C
NM_024675.4(PALB2):c.212-33A>C
NC_000016.10:g.23636367T>G
CM000678.2:g.23636367T>G
NC_000016.9:g.23647688T>G
CM000678.1:g.23647688T>G
NC_000016.8:g.23555189T>G
NG_007406.1:g.9991A>C
ENST00000261584.9:c.212-33A>C
ENST00000261584.8:c.212-33A>C
ENST00000561514.1:c.218-33A>C
ENST00000565038.1:n.86+1483A>C
ENST00000567003.1:n.490-33A>C
ENST00000568219.5:c.-674-33A>C
NM_024675.3:c.212-33A>C

Likely Benign

Met criteria codes 2
BP4 BP7
Not Met criteria codes 1
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.212-33A>C variant in PALB2 is an intronic variant. BP7 applies because the threshold for the application of BP7 to deep intronic acceptor site variants is beyond position -21. The computational splicing predictor SpliceAI gives a score of 0.0 for acceptor loss suggesting that the variant has no impact on splicing. The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006485 in the non-Finnish European population. (PM2_Supporting, BS1, and BA1 are not met). In summary, this variant meets the criteria to be classified as likely 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. (BP4, BP7)
Met criteria codes
BP4
The computational splicing predictor SpliceAI gives a score of 0.0 for acceptor loss suggesting that the variant has no impact on splicing (BP4).
BP7
The c.212-33A>C variant (NM_024675.3) is an intronic variant. BP7 applies because the threshold for the application of BP7 to deep intronic acceptor site variants is beyond position -21.
Not Met criteria codes
PM2
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00006485 (1/15420 genomes) in the non-Finnish European population. (PM2_Supporting, BS1, and BA1 are not met)
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