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Variant: NM_000038.6(APC):c.423-11A>G

CA915943443

824698 (ClinVar)

Gene: APC
Condition: familial adenomatous polyposis 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 1b620616-9505-427d-9ca9-25ef167b55c5
Approved on: 2023-02-18
Published on: 2023-03-14

HGVS expressions

NM_000038.6:c.423-11A>G
NM_000038.6(APC):c.423-11A>G
NC_000005.10:g.112775618A>G
CM000667.2:g.112775618A>G
NC_000005.9:g.112111315A>G
CM000667.1:g.112111315A>G
NC_000005.8:g.112139214A>G
NG_008481.4:g.88098A>G
ENST00000257430.9:c.423-11A>G
ENST00000257430.8:c.423-11A>G
ENST00000507379.5:c.453-11A>G
ENST00000508376.6:c.423-11A>G
ENST00000508624.5:c.423-11A>G
ENST00000512211.6:c.423-11A>G
NM_000038.5:c.423-11A>G
NM_001127510.2:c.423-11A>G
NM_001127511.2:c.453-11A>G
NM_001354895.1:c.423-11A>G
NM_001354896.1:c.423-11A>G
NM_001354897.1:c.453-11A>G
NM_001354898.1:c.348-11A>G
NM_001354899.1:c.423-11A>G
NM_001354900.1:c.246-11A>G
NM_001354901.1:c.246-11A>G
NM_001354902.1:c.453-11A>G
NM_001354903.1:c.423-11A>G
NM_001354904.1:c.348-11A>G
NM_001354905.1:c.246-11A>G
NM_001354906.1:c.-613-11A>G
NM_001127510.3:c.423-11A>G
NM_001127511.3:c.453-11A>G
NM_001354895.2:c.423-11A>G
NM_001354896.2:c.423-11A>G
NM_001354897.2:c.453-11A>G
NM_001354898.2:c.348-11A>G
NM_001354899.2:c.423-11A>G
NM_001354900.2:c.246-11A>G
NM_001354901.2:c.246-11A>G
NM_001354902.2:c.453-11A>G
NM_001354903.2:c.423-11A>G
NM_001354904.2:c.348-11A>G
NM_001354905.2:c.246-11A>G
NM_001354906.2:c.-613-11A>G
More

Likely Pathogenic

The Expert Panel has overridden the computationally generated classification - "Uncertain Significance - Insufficient Evidence"
Met criteria codes 4
PS3_Moderate PM2_Supporting PS4_Moderate PP3
Not Met criteria codes 1
PM5

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP
The c.423-11A>G variant in APC is an intronic variant which substitutes adenine with guanine at position -11 in intron 4. This variant has been reported in 3 probands meeting phenotypic criteria, resulting in a total phenotype score of 2 (PS4_Moderate, Ambry Genetics, Bonn internal data). RT-PCR of this APC variant in patients with FAP showed that it impacted splicing by leading to insertion of the last 10 bp of intron 4 (r.422_423ins423-10_423-1)(p.Ser142Lysfs*3)(PS3_Moderate; PMID21779980, Ambry Genetics, Bonn internal data). The results from 2 in silico splicing predictors indicate that this variant may affect splicing by disrupting the acceptor splice site of intron 4 of APC (PP3). Finally, this variant is absent from gnomAD v2.1.1 (PM2_Supporting). In summary, this variant meets the criteria to be classified as Likely Pathogenic for FAP based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel: PS3_Moderate, PS4_Moderate, PP3 and PM2_supporting (VCEP specifications version 1; date of approval 12/12/2022).
Met criteria codes
PS3_Moderate
RT-PCR of the complete reading frames of APC in patients with FAP showed that the variant c.423-11A>G impacts splicing by leading to insertion of the last 10 bp of intron 3 (p.Ser142Lysfs*3) (PMID21779980). RNA analysis also available from internal data (Ambry Genetics, Bonn University Hospital).
PM2_Supporting
This variant is absent from gnomAD v2.1.1 (PM2_Supporting).
PS4_Moderate
This variant has been reported in 3 probands meeting phenotypic criteria, resulting in a total phenotype score of 2 (PS4_Moderate, Ambry Genetics, Bonn internal data).
PP3
The results from ≥2 in silico splicing predictors (SpliceAI and varSEAK) indicate that this variant may affect splicing by disrupting the acceptor splice site of intron 3 of APC (PP3).
Not Met criteria codes
PM5
No other variant identified at the same nucleotide
Curation History
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