NM_000038.6(APC):c.7704A>G (p.Gly2568=) AND Familial adenomatous polyposis 1

Germline classification:: Benign (4 submissions)
Last evaluated:: Apr 10, 2024
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:: RCV000756996.19

Allele description [Variation Report for NM_000038.6(APC):c.7704A>G (p.Gly2568=)]

NM_000038.6(APC):c.7704A>G (p.Gly2568=)

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.7704A>G (p.Gly2568=)

Other names:

CCDS4107.1:c.7704A>G

HGVS:

NC_000005.10:g.112843298A>G
NG_008481.4:g.155778A>G
NM_000038.6:c.7704A>GMANE SELECT
NM_001127510.3:c.7704A>G
NM_001127511.3:c.7650A>G
NM_001354895.2:c.7704A>G
NM_001354896.2:c.7758A>G
NM_001354897.2:c.7734A>G
NM_001354898.2:c.7629A>G
NM_001354899.2:c.7620A>G
NM_001354900.2:c.7581A>G
NM_001354901.2:c.7527A>G
NM_001354902.2:c.7431A>G
NM_001354903.2:c.7401A>G
NM_001354904.2:c.7326A>G
NM_001354905.2:c.7224A>G
NM_001354906.2:c.6855A>G
NP_000029.2:p.Gly2568=
NP_001120982.1:p.Gly2568=
NP_001120983.2:p.Gly2550=
NP_001341824.1:p.Gly2568=
NP_001341825.1:p.Gly2586=
NP_001341826.1:p.Gly2578=
NP_001341827.1:p.Gly2543=
NP_001341828.1:p.Gly2540=
NP_001341829.1:p.Gly2527=
NP_001341830.1:p.Gly2509=
NP_001341831.1:p.Gly2477=
NP_001341832.1:p.Gly2467=
NP_001341833.1:p.Gly2442=
NP_001341834.1:p.Gly2408=
NP_001341835.1:p.Gly2285=
LRG_130t1:c.7704A>G
LRG_130:g.155778A>G
NC_000005.9:g.112178995A>G
NM_000038.4:c.7704A>G
NM_000038.5:c.7704A>G
NM_001127510.2:c.7704A>G
NP_000029.2:p.(=)
c.7704A>G
p.G2568G
p.Gly2568Gly

Links:

dbSNP: rs35043160

NCBI 1000 Genomes Browser:

rs35043160

Molecular consequence:

NM_000038.6:c.7704A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127510.3:c.7704A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001127511.3:c.7650A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354895.2:c.7704A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354896.2:c.7758A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354897.2:c.7734A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354898.2:c.7629A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354899.2:c.7620A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354900.2:c.7581A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354901.2:c.7527A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354902.2:c.7431A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354903.2:c.7401A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354904.2:c.7326A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354905.2:c.7224A>G - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001354906.2:c.6855A>G - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Familial adenomatous polyposis 1 (FAP1)
Synonyms:: POLYPOSIS, ADENOMATOUS INTESTINAL; FAMILIAL ADENOMATOUS POLYPOSIS 1, ATTENUATED; APC-Associated Polyposis Conditions
Identifiers:: MONDO: MONDO:0021056; MedGen: C2713442; OMIM: 175100

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PREDICTED: uncharacterized protein LOC103499638 [Cucumis melo]
PREDICTED: uncharacterized protein LOC103499638 [Cucumis melo]
gi|659121948|ref|XP_008460897.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000562618	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Feb 1, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000591214	Department of Pathology and Laboratory Medicine, Sinai Health System - The Canadian Open Genetics Repository (COGR) See additional submitters Franklin by Genoox	no assertion criteria provided	Benign	unknown	clinical testing
SCV004017694	KCCC/NGS Laboratory, Kuwait Cancer Control Center	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign (Jul 7, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005084444	Myriad Genetics, Inc.	criteria provided, single submitter (Myriad Autosomal Dominant, Autosomal Recessive and X-Linked Classification Criteria (2023))	Benign (Apr 10, 2024)	unknown	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
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
not provided	unknown	yes	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000562618.9

#	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), SCV000591214.2

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

Description

The p.Gly2568Gly variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. This variant was not identified in the literature, nor was it identified in the HGMD, UMD or LOVD databases. This variant was reported in dbSNP (ID#rs35043160), in the 1000 Genomes Project with a frequency of 0.027, and in the Exome Variant Server ESP Project with frequencies of 0.0002 in European American alleles and 0.097 in African American alleles, increasing the likelihood that this is a low frequency benign variant in certain populations of origin. In summary, based on the above information, this variant is classified as benign.

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

From KCCC/NGS Laboratory, Kuwait Cancer Control Center, SCV004017694.1

#	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 Myriad Genetics, Inc., SCV005084444.1

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

Description

This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing.

#	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: Oct 26, 2024

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