NM_003839.4(TNFRSF11A):c.56C>T (p.Ala19Val) AND not provided

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

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 19, 2022
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:: RCV002048872.5

Allele description

NM_003839.4(TNFRSF11A):c.56C>T (p.Ala19Val)

Gene:

TNFRSF11A:TNF receptor superfamily member 11a [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

18q21.33

Genomic location:

Preferred name:

NM_003839.4(TNFRSF11A):c.56C>T (p.Ala19Val)

HGVS:

NC_000018.10:g.62325408C>T
NG_008098.1:g.5094C>T
NM_001270949.2:c.56C>T
NM_001270950.2:c.56C>T
NM_001270951.2:c.56C>T
NM_001278268.2:c.56C>T
NM_003839.4:c.56C>TMANE SELECT
NP_001257878.1:p.Ala19Val
NP_001257879.1:p.Ala19Val
NP_001257880.1:p.Ala19Val
NP_001265197.1:p.Ala19Val
NP_003830.1:p.Ala19Val
LRG_194:g.5094C>T
NC_000018.9:g.59992641C>T

Protein change:

A19V

Links:

dbSNP: rs1198549517

NCBI 1000 Genomes Browser:

rs1198549517

Molecular consequence:

NM_001270949.2:c.56C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001270950.2:c.56C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001270951.2:c.56C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001278268.2:c.56C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003839.4:c.56C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV002310279	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 19, 2022)	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

SCV002310279

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 19, 2022)

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 Invitae, SCV002310279.3

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

Description

This variant has not been reported in the literature in individuals affected with TNFRSF11A-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1523255). This variant is present in population databases (no rsID available, gnomAD 0.007%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 19 of the TNFRSF11A protein (p.Ala19Val).

#	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 28, 2024

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Relating variation to medicine