NM_003924.4(PHOX2B):c.450C>G (p.Arg150=) AND not provided

Germline classification:: Benign/Likely benign (2 submissions)
Last evaluated:: Mar 23, 2020
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:: RCV000588386.5

Allele description [Variation Report for NM_003924.4(PHOX2B):c.450C>G (p.Arg150=)]

NM_003924.4(PHOX2B):c.450C>G (p.Arg150=)

Gene:

PHOX2B:paired like homeobox 2B [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

4p13

Genomic location:

Preferred name:

NM_003924.4(PHOX2B):c.450C>G (p.Arg150=)

HGVS:

NC_000004.12:g.41746302G>C
NG_008243.1:g.7669C>G
NM_003924.4:c.450C>GMANE SELECT
NP_003915.2:p.Arg150=
NP_003915.2:p.Arg150=
LRG_513t1:c.450C>G
LRG_513:g.7669C>G
LRG_513p1:p.Arg150=
NC_000004.11:g.41748319G>C
NM_003924.3:c.450C>G
p.Arg150Arg

Links:

dbSNP: rs17881486

NCBI 1000 Genomes Browser:

rs17881486

Molecular consequence:

NM_003924.4:c.450C>G - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV000698218	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (May 17, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001804568	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (Mar 23, 2020)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000698218

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(May 17, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001804568

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(Mar 23, 2020)

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	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698218.1

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

Description

Variant summary: The PHOX2B c.450C>G (p.Arg150Arg) variant causes a synonymous change involving a non-conserved nucleotide with 5/5 splice prediction tools calculating no significant effect on splicing, although these predictions have yet to be functionally assessed. This variant was found in the large, broad control population, ExAC, with an allele frequency of 134/117664 (1 homozygote, 1/877, frequency: 0.001139), predominantly observed in the African cohort, 129/9668 (1 homozygote, 1/74, frequency: 0.01334), which significantly exceeds the estimated the maximal expected allele frequency for a pathogenic PHOX2B variant of 1/1250000 (0.0000008). Therefore, suggesting the variant is a common polymorphism found in population(s) of African origin. Therefore, taking all available lines of evidence into consideration, the variant of interest is classified as Benign.

#	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 GeneDx, SCV001804568.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: May 1, 2024

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