NM_000038.6(APC):c.4479G>A (p.Thr1493=) AND not specified

This record was updated by the submitter. Please see the current version.

Germline classification:: Benign (6 submissions)
Last evaluated:: Jul 6, 2018
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:: RCV000035071.12

Allele description

NM_000038.6(APC):c.4479G>A (p.Thr1493=)

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.4479G>A (p.Thr1493=)

HGVS:

NC_000005.10:g.112840073G>A
NG_008481.4:g.152553G>A
NM_000038.6:c.4479G>AMANE SELECT
NM_001127510.3:c.4479G>A
NM_001127511.3:c.4425G>A
NM_001354895.2:c.4479G>A
NM_001354896.2:c.4533G>A
NM_001354897.2:c.4509G>A
NM_001354898.2:c.4404G>A
NM_001354899.2:c.4395G>A
NM_001354900.2:c.4356G>A
NM_001354901.2:c.4302G>A
NM_001354902.2:c.4206G>A
NM_001354903.2:c.4176G>A
NM_001354904.2:c.4101G>A
NM_001354905.2:c.3999G>A
NM_001354906.2:c.3630G>A
NP_000029.2:p.Thr1493=
NP_001120982.1:p.Thr1493=
NP_001120983.2:p.Thr1475=
NP_001341824.1:p.Thr1493=
NP_001341825.1:p.Thr1511=
NP_001341826.1:p.Thr1503=
NP_001341827.1:p.Thr1468=
NP_001341828.1:p.Thr1465=
NP_001341829.1:p.Thr1452=
NP_001341830.1:p.Thr1434=
NP_001341831.1:p.Thr1402=
NP_001341832.1:p.Thr1392=
NP_001341833.1:p.Thr1367=
NP_001341834.1:p.Thr1333=
NP_001341835.1:p.Thr1210=
LRG_130t1:c.4479G>A
LRG_130:g.152553G>A
NC_000005.8:g.112203669G>A
NC_000005.9:g.112175770G>A
NM_000038.4:c.4479G>A
NM_000038.5:c.4479G>A
NM_001127510.2:c.4479G>A
NP_000029.2:p.(=)
c.4479G>A
p.T1493T

Links:

dbSNP: rs41115

NCBI 1000 Genomes Browser:

rs41115

Molecular consequence:

NM_000038.6:c.4479G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127510.3:c.4479G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127511.3:c.4425G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354895.2:c.4479G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354896.2:c.4533G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354897.2:c.4509G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354898.2:c.4404G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354899.2:c.4395G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354900.2:c.4356G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354901.2:c.4302G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354902.2:c.4206G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354903.2:c.4176G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354904.2:c.4101G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354905.2:c.3999G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354906.2:c.3630G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000058711	Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine	no assertion criteria provided	Benign (Mar 1, 2008)	germline	clinical testing
SCV000109824	EGL Genetic Diagnostics, Eurofins Clinical Diagnostics	criteria provided, single submitter (EGL Classification Definitions 2015)	Benign (Mar 16, 2016)	germline	clinical testing	Citation Link,
SCV000256997	Mayo Clinic Genetic Testing Laboratories,Mayo Clinic	no assertion criteria provided	Benign	unknown	research
SCV000301595	PreventionGenetics,PreventionGenetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000591174	Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Apr 27, 2012)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000602515	ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Benign (Jul 6, 2018)	germline	clinical testing	Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	29	29	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	71	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	17	not provided	not provided	not provided	not provided	research

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine, SCV000058711.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	29	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		29	not provided	29	not provided

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000109824.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	71	not provided	not provided	clinical testing	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		71	not provided	not provided	not provided

From Mayo Clinic Genetic Testing Laboratories,Mayo Clinic, SCV000256997.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	17	not provided	not provided	research	not provided

#	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		17	not provided	not provided	not provided

From PreventionGenetics,PreventionGenetics, SCV000301595.1

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV000591174.1

#	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	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories, SCV000602515.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	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: Mar 12, 2021

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