NM_000038.6(APC):c.7130_7144del (p.Asn2377_Gln2381del) AND Hereditary cancer-predisposing syndrome

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jun 2, 2021
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000561992.12

Allele description [Variation Report for NM_000038.6(APC):c.7130_7144del (p.Asn2377_Gln2381del)]

NM_000038.6(APC):c.7130_7144del (p.Asn2377_Gln2381del)

Gene:

APC:APC regulator of WNT signaling pathway [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_000038.6(APC):c.7130_7144del (p.Asn2377_Gln2381del)

HGVS:

NC_000005.10:g.112842724_112842738del
NG_008481.4:g.155204_155218del
NM_000038.6:c.7130_7144delMANE SELECT
NM_001127510.3:c.7130_7144del
NM_001127511.3:c.7076_7090del
NM_001354895.2:c.7130_7144del
NM_001354896.2:c.7184_7198del
NM_001354897.2:c.7160_7174del
NM_001354898.2:c.7055_7069del
NM_001354899.2:c.7046_7060del
NM_001354900.2:c.7007_7021del
NM_001354901.2:c.6953_6967del
NM_001354902.2:c.6857_6871del
NM_001354903.2:c.6827_6841del
NM_001354904.2:c.6752_6766del
NM_001354905.2:c.6650_6664del
NM_001354906.2:c.6281_6295del
NP_000029.2:p.Asn2377_Gln2381del
NP_001120982.1:p.Asn2377_Gln2381del
NP_001120983.2:p.Asn2359_Gln2363del
NP_001341824.1:p.Asn2377_Gln2381del
NP_001341825.1:p.Asn2395_Gln2399del
NP_001341826.1:p.Asn2387_Gln2391del
NP_001341827.1:p.Asn2352_Gln2356del
NP_001341828.1:p.Asn2349_Gln2353del
NP_001341829.1:p.Asn2336_Gln2340del
NP_001341830.1:p.Asn2318_Gln2322del
NP_001341831.1:p.Asn2286_Gln2290del
NP_001341832.1:p.Asn2276_Gln2280del
NP_001341833.1:p.Asn2251_Gln2255del
NP_001341834.1:p.Asn2217_Gln2221del
NP_001341835.1:p.Asn2094_Gln2098del
LRG_130t1:c.7130_7144del
LRG_130:g.155204_155218del
NC_000005.9:g.112178420_112178434del
NC_000005.9:g.112178421_112178435del
NM_000038.4:c.7130_7144delACCTTACCAAACAAA
NM_000038.5:c.7130_7144del15

Links:

dbSNP: rs1472879431

NCBI 1000 Genomes Browser:

rs1472879431

Molecular consequence:

NM_000038.6:c.7130_7144del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127510.3:c.7130_7144del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001127511.3:c.7076_7090del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354895.2:c.7130_7144del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354896.2:c.7184_7198del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354897.2:c.7160_7174del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354898.2:c.7055_7069del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354899.2:c.7046_7060del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354900.2:c.7007_7021del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354901.2:c.6953_6967del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354902.2:c.6857_6871del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354903.2:c.6827_6841del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354904.2:c.6752_6766del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354905.2:c.6650_6664del - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001354906.2:c.6281_6295del - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Hereditary cancer-predisposing syndrome
Synonyms:: Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000667479	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Nov 5, 2020)	germline	clinical testing	Citation Link,
SCV002527446	Sema4, Sema4	criteria provided, single submitter (Sema4 Curation Guidelines)	Uncertain significance (Jun 2, 2021)	germline	curation	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000667479

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Nov 5, 2020)

germline

clinical testing

Citation Link,

SCV002527446

Sema4, Sema4

criteria provided, single submitter

(Sema4 Curation Guidelines)

Uncertain significance
(Jun 2, 2021)

germline

curation

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Ambry Genetics, SCV000667479.5

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

Description

The c.7130_7144del15 variant (also known as p.N2377_Q2381del) is located in coding exon 15 of the APC gene. This variant results from an in-frame ACCTTACCAAACAAA deletion at nucleotide positions 7130 to 7144. This results in the deletion of five amino acids between codons 2377 and 2381. This region is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive (Choi Y et al. PLoS ONE. 2012; 7(10):e46688). Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

From Sema4, Sema4, SCV002527446.1

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

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

Last Updated: Oct 26, 2024

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