NM_052945.4(TNFRSF13C):c.102C>T (p.Ala34=) AND Immunodeficiency, common variable, 4

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

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 2, 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:: RCV000968902.15

Allele description

NM_052945.4(TNFRSF13C):c.102C>T (p.Ala34=)

Genes:

LOC130067574:ATAC-STARR-seq lymphoblastoid silent region 13813 [Gene]
TNFRSF13C:TNF receptor superfamily member 13C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

22q13.2

Genomic location:

Preferred name:

NM_052945.4(TNFRSF13C):c.102C>T (p.Ala34=)

HGVS:

NC_000022.11:g.41926672G>A
NG_007579.1:g.5146C>T
NM_052945.4:c.102C>TMANE SELECT
NP_443177.1:p.Ala34=
NP_443177.1:p.Ala34=
LRG_184t1:c.102C>T
LRG_184:g.5146C>T
LRG_184p1:p.Ala34=
NC_000022.10:g.42322676G>A
NM_052945.3:c.102C>T

Links:

dbSNP: rs567541615

NCBI 1000 Genomes Browser:

rs567541615

Molecular consequence:

NM_052945.4:c.102C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Immunodeficiency, common variable, 4
Synonyms:: ANTIBODY DEFICIENCY DUE TO BAFFR DEFECT
Identifiers:: MONDO: MONDO:0013284; MedGen: C3150739; Orphanet: 1572; OMIM: 613494

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001116386	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 2, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002506097	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Likely benign (Feb 8, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001116386

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 2, 2024)

germline

clinical testing

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

SCV002506097

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)

Likely benign
(Feb 8, 2022)

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	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, SCV001116386.6

#	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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002506097.2

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Aug 11, 2024

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