NM_003070.5(SMARCA2):c.669GCA[8] (p.Gln234_Gln238del) AND not provided

Germline classification:: Benign/Likely benign (6 submissions)
Last evaluated:: Dec 1, 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:: RCV000513731.27

Allele description [Variation Report for NM_003070.5(SMARCA2):c.669GCA[8] (p.Gln234_Gln238del)]

NM_003070.5(SMARCA2):c.669GCA[8] (p.Gln234_Gln238del)

Gene:

SMARCA2:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

9p24.3

Genomic location:

Preferred name:

NM_003070.5(SMARCA2):c.669GCA[8] (p.Gln234_Gln238del)

HGVS:

NC_000009.12:g.2039779GCA[8]
NG_032162.2:g.64490GCA[8]
NG_115850.1:g.121GCA[8]
NM_001289396.2:c.669_671GCA[8]
NM_001289397.2:c.669GCA[8]
NM_003070.5:c.669GCA[8]MANE SELECT
NM_139045.4:c.669GCA[8]
NP_001276325.1:p.Gln234_Gln238del
NP_001276325.1:p.Gln234_Gln238del
NP_001276326.1:p.Gln234_Gln238del
NP_003061.3:p.Gln234_Gln238del
NP_620614.2:p.Gln234_Gln238del
LRG_882t1:c.669GCA[8]
LRG_882:g.64490GCA[8]
LRG_882p1:p.Gln234_Gln238del
NC_000009.11:g.2039777_2039791del
NC_000009.11:g.2039779GCA[8]
NM_001289396.1:c.669GCA[8]
NM_003070.3:c.693_707del
NM_003070.3:c.693_707del15

Links:

dbSNP: rs113070757

NCBI 1000 Genomes Browser:

rs113070757

Molecular consequence:

NM_001289397.2:c.669GCA[8] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_003070.5:c.669GCA[8] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_139045.4:c.669GCA[8] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001289396.2:c.669_671GCA[8] - inframe_indel - [Sequence Ontology: SO:0001820]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000610423	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Aug 29, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001741258	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001799795	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001907122	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Nov 5, 2018)	germline	clinical testing	Citation Link,
SCV002466122	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jul 18, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002564030	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Benign (Dec 1, 2023)	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	yes	17	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	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing

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

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, SCV000610423.1

#	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	not provided	not provided	not provided	not provided		not provided	0.002309	not provided	not provided

From Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen - VKGL Data-share Consensus, SCV001741258.3

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

From Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) - VKGL Data-share Consensus, SCV001799795.1

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

From GeneDx, SCV001907122.1

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

From Invitae, SCV002466122.3

#	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 CeGaT Center for Human Genetics Tuebingen, SCV002564030.11

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

Description

SMARCA2: BS1, BS2

#	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		17	not provided	not provided	not provided

Last Updated: Jun 2, 2024

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