NM_003073.5(SMARCB1):c.438A>G (p.Pro146=) AND not provided

Clinical significance:Benign/Likely benign (Last evaluated: Dec 8, 2020)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
4 submissions [Details]
Record status:
current
Accession:
RCV000587734.7

Allele description [Variation Report for NM_003073.5(SMARCB1):c.438A>G (p.Pro146=)]

NM_003073.5(SMARCB1):c.438A>G (p.Pro146=)

Gene:
SMARCB1:SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily b, member 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
22q11.23
Genomic location:
Preferred name:
NM_003073.5(SMARCB1):c.438A>G (p.Pro146=)
HGVS:
  • NC_000022.11:g.23801019A>G
  • NG_009303.1:g.19057A>G
  • NM_001007468.3:c.411A>G
  • NM_001317946.2:c.411A>G
  • NM_001362877.2:c.438A>G
  • NM_003073.5:c.438A>GMANE SELECT
  • NP_001007469.1:p.Pro137=
  • NP_001304875.1:p.Pro137=
  • NP_001349806.1:p.Pro146=
  • NP_003064.2:p.Pro146=
  • LRG_520t1:c.438A>G
  • LRG_520:g.19057A>G
  • NC_000022.10:g.24143206A>G
  • NM_003073.3:c.438A>G
Links:
dbSNP: rs35105793
NCBI 1000 Genomes Browser:
rs35105793
Molecular consequence:
  • NM_001007468.3:c.411A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001317946.2:c.411A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001362877.2:c.438A>G - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_003073.5:c.438A>G - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
2

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000287851Invitaecriteria provided, single submitter
Benign
(Dec 8, 2020)
germlineclinical testing

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

SCV000698160Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(May 25, 2016)
germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001334885CeGaT Praxis fuer Humangenetik Tuebingencriteria provided, single submitter
Likely benign
(Apr 1, 2020)
germlineclinical testing

Citation Link,

SCV001827831GeneDxno assertion criteria provided
Benign
(Aug 18, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000287851.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698160.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The SMARCB1 c.438A>G (p.Pro146Pro) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 5/5 splice prediction tools in Alamut predict no change to normal splicing. This variant was found in 193/121404 control chromosomes (including 3 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0167211 (174/10406). This frequency is significantly greater than the estimated maximal expected allele frequency of a pathogenic SMARCB1 variant (0.0000001), highly suggesting this is a benign polymorphism found primarily in populations of African origin. Based on the synonymous nature of this variant and the high allele frequency in the general population, this variant is classified as Benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From CeGaT Praxis fuer Humangenetik Tuebingen, SCV001334885.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From GeneDx, SCV001827831.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 7, 2021

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