NM_003070.5(SMARCA2):c.3458A>T (p.Asp1153Val) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jun 29, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003557275.2

Allele description [Variation Report for NM_003070.5(SMARCA2):c.3458A>T (p.Asp1153Val)]

NM_003070.5(SMARCA2):c.3458A>T (p.Asp1153Val)

Gene:

SMARCA2:SWI/SNF related BAF chromatin remodeling complex subunit ATPase 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9p24.3

Genomic location:

Preferred name:

NM_003070.5(SMARCA2):c.3458A>T (p.Asp1153Val)

HGVS:

NC_000009.12:g.2115823A>T
NG_032162.2:g.140534A>T
NM_001289396.2:c.3458A>T
NM_001289397.2:c.3284A>T
NM_003070.5:c.3458A>TMANE SELECT
NM_139045.4:c.3458A>T
NP_001276325.1:p.Asp1153Val
NP_001276325.1:p.Asp1153Val
NP_001276326.1:p.Asp1095Val
NP_003061.3:p.Asp1153Val
NP_620614.2:p.Asp1153Val
LRG_882t1:c.3458A>T
LRG_882:g.140534A>T
LRG_882p1:p.Asp1153Val
NC_000009.11:g.2115823A>T
NM_001289396.1:c.3458A>T

Protein change:

D1095V

Molecular consequence:

NM_001289396.2:c.3458A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001289397.2:c.3284A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003070.5:c.3458A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_139045.4:c.3458A>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Pasteurella bettyae CCUG 2042 contig00008, whole genome shotgun sequence
Pasteurella bettyae CCUG 2042 contig00008, whole genome shotgun sequence
gi|387770573|ref|NZ_AJSX01000034.1| WGS:NZ_AJSX01|contig00008

Nucleotide
Annotated Genomic for Nucleotide (Select 1677482729) (2)
Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004283492	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jun 29, 2023)	germline	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

SCV004283492

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jun 29, 2023)

germline

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

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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004283492.1

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 1153 of the SMARCA2 protein (p.Asp1153Val). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant has not been reported in the literature in individuals affected with SMARCA2-related conditions. This variant is not present in population databases (gnomAD no frequency). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Feb 1, 2025

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