NM_001250.6(CD40):c.606C>T (p.Phe202=) AND Hyper-IgM syndrome type 3

Germline classification:: Benign (2 submissions)
Last evaluated:: Nov 29, 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:: RCV001000341.13

Allele description [Variation Report for NM_001250.6(CD40):c.606C>T (p.Phe202=)]

NM_001250.6(CD40):c.606C>T (p.Phe202=)

Gene:

CD40:CD40 molecule [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20q13.12

Genomic location:

Preferred name:

NM_001250.6(CD40):c.606C>T (p.Phe202=)

HGVS:

NC_000020.11:g.46128184C>T
NG_007279.1:g.14918C>T
NM_001250.6:c.606C>TMANE SELECT
NM_001302753.2:c.646C>T
NM_001322421.2:c.606C>T
NM_001322422.2:c.450C>T
NM_001362758.2:c.606C>T
NM_152854.4:c.544C>T
NP_001241.1:p.Phe202=
NP_001289682.1:p.Arg216Trp
NP_001309350.1:p.Phe202=
NP_001309351.1:p.Phe150=
NP_001349687.1:p.Phe202=
NP_690593.1:p.Arg182Trp
LRG_40t1:c.606C>T
LRG_40:g.14918C>T
NC_000020.10:g.44756823C>T
NM_001250.4:c.606C>T
NR_126502.2:n.639C>T
NR_136327.2:n.542C>T

Protein change:

R182W

Links:

dbSNP: rs7273698

NCBI 1000 Genomes Browser:

rs7273698

Molecular consequence:

NM_001302753.2:c.646C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_152854.4:c.544C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_126502.2:n.639C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_136327.2:n.542C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001250.6:c.606C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322421.2:c.606C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322422.2:c.450C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001362758.2:c.606C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Name:: Hyper-IgM syndrome type 3
Synonyms:: Immunodeficiency with hyper IgM type 3; Hyper-IgM Immunodeficiency Syndrome, Type 3
Identifiers:: MONDO: MONDO:0011735; MedGen: C1720957; OMIM: 606843

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000434130	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Benign (Jan 12, 2018)	germline	clinical testing	Citation Link,
SCV001157070	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Benign (Nov 29, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000434130

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Benign
(Jan 12, 2018)

germline

clinical testing

Citation Link,

SCV001157070

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2024)

Benign
(Nov 29, 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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000434130.3

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

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

#	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, SCV001157070.3

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

Last Updated: Sep 29, 2024

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