Clinical, splicing, and functional analysis to classify BRCA2 exon 3 variants: Application of a points-based ACMG/AMP approach
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Clinical, splicing, and functional analysis to classify BRCA2 exon 3 variants : Application of a points-based ACMG/AMP approach. / Thomassen, Mads; Mesman, Romy L. S.; Hansen, Thomas V. O.; Menendez, Mireia; Rossing, Maria; Esteban-Sánchez, Ada; Tudini, Emma; Törngren, Therese; Parsons, Michael T.; Pedersen, Inge S.; Teo, Soo H.; Kruse, Torben A.; Møller, Pål; Borg, Åke; Jensen, Uffe B.; Christensen, Lise L.; Singer, Christian F.; Muhr, Daniela; Santamarina, Marta; Brandao, Rita; Andresen, Brage S.; Feng, Bing-Jian; Canson, Daffodil; Richardson, Marcy E.; Karam, Rachid; Pesaran, Tina; LaDuca, Holly; Conner, Blair R.; Abualkheir, Nelly; Hoang, Lily; Calléja, Fabienne M G R; Andrews, Lesley; James, Paul A.; Bunyan, Dave; Hamblett, Amanda; Radice, Paolo; Goldgar, David E.; Walker, Logan C.; Engel, Christoph; Claes, Kathleen B. M.; Macháčková, Eva; Baralle, Diana; Viel, Alessandra; Wappenschmidt, Barbara; Lazaro, Conxi; Vega, Ana; Vreeswijk, Maaike P G; de la Hoya, Miguel; Spurdle, Amanda B.; ENIGMA Consortium.
In: Human Mutation, Vol. 43, No. 12, 2022, p. 1921-1944.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Clinical, splicing, and functional analysis to classify BRCA2 exon 3 variants
T2 - Application of a points-based ACMG/AMP approach
AU - Thomassen, Mads
AU - Mesman, Romy L. S.
AU - Hansen, Thomas V. O.
AU - Menendez, Mireia
AU - Rossing, Maria
AU - Esteban-Sánchez, Ada
AU - Tudini, Emma
AU - Törngren, Therese
AU - Parsons, Michael T.
AU - Pedersen, Inge S.
AU - Teo, Soo H.
AU - Kruse, Torben A.
AU - Møller, Pål
AU - Borg, Åke
AU - Jensen, Uffe B.
AU - Christensen, Lise L.
AU - Singer, Christian F.
AU - Muhr, Daniela
AU - Santamarina, Marta
AU - Brandao, Rita
AU - Andresen, Brage S.
AU - Feng, Bing-Jian
AU - Canson, Daffodil
AU - Richardson, Marcy E.
AU - Karam, Rachid
AU - Pesaran, Tina
AU - LaDuca, Holly
AU - Conner, Blair R.
AU - Abualkheir, Nelly
AU - Hoang, Lily
AU - Calléja, Fabienne M G R
AU - Andrews, Lesley
AU - James, Paul A.
AU - Bunyan, Dave
AU - Hamblett, Amanda
AU - Radice, Paolo
AU - Goldgar, David E.
AU - Walker, Logan C.
AU - Engel, Christoph
AU - Claes, Kathleen B. M.
AU - Macháčková, Eva
AU - Baralle, Diana
AU - Viel, Alessandra
AU - Wappenschmidt, Barbara
AU - Lazaro, Conxi
AU - Vega, Ana
AU - Vreeswijk, Maaike P G
AU - de la Hoya, Miguel
AU - Spurdle, Amanda B.
AU - ENIGMA Consortium
N1 - Publisher Copyright: © 2022 The Authors. Human Mutation published by Wiley Periodicals LLC.
PY - 2022
Y1 - 2022
N2 - Skipping of BRCA2 exon 3 (∆E3) is a naturally occurring splicing event, complicating clinical classification of variants that may alter ∆E3 expression. This study used multiple evidence types to assess pathogenicity of 85 variants in/near BRCA2 exon 3. Bioinformatically predicted spliceogenic variants underwent mRNA splicing analysis using minigenes and/or patient samples. ∆E3 was measured using quantitative analysis. A mouse embryonic stem cell (mESC) based assay was used to determine the impact of 18 variants on mRNA splicing and protein function. For each variant, population frequency, bioinformatic predictions, clinical data, and existing mRNA splicing and functional results were collated. Variant class was assigned using a gene-specific adaptation of ACMG/AMP guidelines, following a recently proposed points-based system. mRNA and mESC analysis combined identified six variants with transcript and/or functional profiles interpreted as loss of function. Cryptic splice site use for acceptor site variants generated a transcript encoding a shorter protein that retains activity. Overall, 69/85 (81%) variants were classified using the points-based approach. Our analysis shows the value of applying gene-specific ACMG/AMP guidelines using a points-based approach and highlights the consideration of cryptic splice site usage to appropriately assign PVS1 code strength.
AB - Skipping of BRCA2 exon 3 (∆E3) is a naturally occurring splicing event, complicating clinical classification of variants that may alter ∆E3 expression. This study used multiple evidence types to assess pathogenicity of 85 variants in/near BRCA2 exon 3. Bioinformatically predicted spliceogenic variants underwent mRNA splicing analysis using minigenes and/or patient samples. ∆E3 was measured using quantitative analysis. A mouse embryonic stem cell (mESC) based assay was used to determine the impact of 18 variants on mRNA splicing and protein function. For each variant, population frequency, bioinformatic predictions, clinical data, and existing mRNA splicing and functional results were collated. Variant class was assigned using a gene-specific adaptation of ACMG/AMP guidelines, following a recently proposed points-based system. mRNA and mESC analysis combined identified six variants with transcript and/or functional profiles interpreted as loss of function. Cryptic splice site use for acceptor site variants generated a transcript encoding a shorter protein that retains activity. Overall, 69/85 (81%) variants were classified using the points-based approach. Our analysis shows the value of applying gene-specific ACMG/AMP guidelines using a points-based approach and highlights the consideration of cryptic splice site usage to appropriately assign PVS1 code strength.
KW - ACMG/AMP classification
KW - BRCA2
KW - dPCR
KW - functional analysis
KW - quantitation
KW - splicing
U2 - 10.1002/humu.24449
DO - 10.1002/humu.24449
M3 - Journal article
C2 - 35979650
AN - SCOPUS:85140357391
VL - 43
SP - 1921
EP - 1944
JO - Human Mutation
JF - Human Mutation
SN - 1059-7794
IS - 12
ER -
ID: 329441049