NM_000038.6(APC):c.8061A>G (p.Ser2687=) AND not provided

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Aug 30, 2023
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:: RCV000586668.13

Allele description [Variation Report for NM_000038.6(APC):c.8061A>G (p.Ser2687=)]

NM_000038.6(APC):c.8061A>G (p.Ser2687=)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

5q22.2

Genomic location:

Preferred name:

NM_000038.6(APC):c.8061A>G (p.Ser2687=)

HGVS:

NC_000005.10:g.112843655A>G
NG_008481.4:g.156135A>G
NM_000038.6:c.8061A>GMANE SELECT
NM_001127510.3:c.8061A>G
NM_001127511.3:c.8007A>G
NM_001354895.2:c.8061A>G
NM_001354896.2:c.8115A>G
NM_001354897.2:c.8091A>G
NM_001354898.2:c.7986A>G
NM_001354899.2:c.7977A>G
NM_001354900.2:c.7938A>G
NM_001354901.2:c.7884A>G
NM_001354902.2:c.7788A>G
NM_001354903.2:c.7758A>G
NM_001354904.2:c.7683A>G
NM_001354905.2:c.7581A>G
NM_001354906.2:c.7212A>G
NP_000029.2:p.Ser2687=
NP_001120982.1:p.Ser2687=
NP_001120983.2:p.Ser2669=
NP_001341824.1:p.Ser2687=
NP_001341825.1:p.Ser2705=
NP_001341826.1:p.Ser2697=
NP_001341827.1:p.Ser2662=
NP_001341828.1:p.Ser2659=
NP_001341829.1:p.Ser2646=
NP_001341830.1:p.Ser2628=
NP_001341831.1:p.Ser2596=
NP_001341832.1:p.Ser2586=
NP_001341833.1:p.Ser2561=
NP_001341834.1:p.Ser2527=
NP_001341835.1:p.Ser2404=
LRG_130:g.156135A>G
NC_000005.9:g.112179352A>G
NM_000038.5:c.8061A>G

Links:

dbSNP: rs746180965

NCBI 1000 Genomes Browser:

rs746180965

Molecular consequence:

NM_000038.6:c.8061A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127510.3:c.8061A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127511.3:c.8007A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354895.2:c.8061A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354896.2:c.8115A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354897.2:c.8091A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354898.2:c.7986A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354899.2:c.7977A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354900.2:c.7938A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354901.2:c.7884A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354902.2:c.7788A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354903.2:c.7758A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354904.2:c.7683A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354905.2:c.7581A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354906.2:c.7212A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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biosample
Bos taurus isolate Cin15 mitochondrion, complete genome
Bos taurus isolate Cin15 mitochondrion, complete genome
gi|355330817|gb|JN817318.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000694135	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely benign (May 22, 2017)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001470667	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Likely benign (Aug 30, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000694135

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely benign
(May 22, 2017)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001470667

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Likely benign
(Aug 30, 2023)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000694135.1

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

Description

Variant summary: The APC c.8061A>G (p.Ser2687Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 3/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 4/121330 control chromosomes, predominantly observed in the Latino subpopulation at a frequency of 0.000259 (3/11574). This frequency is about 4 times the estimated maximal expected allele frequency of a pathogenic APC variant (0.0000714), suggesting this is likely a benign polymorphism found primarily in the populations of Latino origin. In addition, one other clinical diagnostic laboratory classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as likely benign.

#	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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV001470667.2

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

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

Last Updated: Sep 16, 2024

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