NM_003924.4(PHOX2B):c.756_776del (p.Ala254_Ala260del) AND not provided

Germline classification:: Benign (2 submissions)
Last evaluated:: May 4, 2022
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:: RCV000587639.4

Allele description [Variation Report for NM_003924.4(PHOX2B):c.756_776del (p.Ala254_Ala260del)]

NM_003924.4(PHOX2B):c.756_776del (p.Ala254_Ala260del)

Genes:

PHOX2B:paired like homeobox 2B [Gene - OMIM - HGNC]
LOC110011216:paired like homeobox 2b polyalanine repeat instability region [Gene]

Variant type:

Deletion

Cytogenetic location:

4p13

Genomic location:

Preferred name:

NM_003924.4(PHOX2B):c.756_776del (p.Ala254_Ala260del)

HGVS:

NC_000004.11:g.41747993_41748013del
NC_000004.12:g.41745990_41746010del
NG_008243.1:g.7975_7995del
NG_053075.1:g.116_136del
NM_003924.4:c.756_776delMANE SELECT
NP_003915.2:p.Ala254_Ala260del
NP_003915.2:p.Ala254_Ala260del
LRG_513t1:c.756_776del
LRG_513:g.7975_7995del
LRG_513p1:p.Ala254_Ala260del
NC_000004.11:g.41747993_41748013del
NC_000004.11:g.41747993_41748013delGCCGCCGCTGCCGCTGCCGCC
NC_000004.11:g.41748007_41748027del
NC_000004.11:g.41748007_41748027del
NM_003924.3:c.756_776del
NM_003924.3:c.756_776del
NM_003924.3:c.756_776del21
NM_003924.3:c.756_776del21
NM_003924.3:c.756_776delGGCGGCAGCGGCAGCGGCGGC

Links:

dbSNP: rs17879189

NCBI 1000 Genomes Browser:

rs17879189

Molecular consequence:

NM_003924.4:c.756_776del - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000698217	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,
SCV003799603	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2021)	Benign (May 4, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000698217

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,

SCV003799603

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)

Benign
(May 4, 2022)

germline

clinical testing

Citation Link

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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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698217.1

#	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.756_776delGGCGGCAGCGGCAGCGGCGGC (p.Ala253_Ala259del) variant causes an in-frame deletion within a repetitive alanine region. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 318/24632 control chromosomes (10 homozygotes, 1/77, frequency: 0.01291), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic PHOX2B variant of 1/1250000 (0.0000008), suggesting this variant is a benign polymorphism. Therefore, 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 ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV003799603.2

#	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: Oct 13, 2024

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