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NM_003924.4(PHOX2B):c.234C>T (p.Tyr78=) AND not provided

Germline classification:
Benign (1 submission)
Last evaluated:
May 17, 2016
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:
RCV000590552.3

Allele description [Variation Report for NM_003924.4(PHOX2B):c.234C>T (p.Tyr78=)]

NM_003924.4(PHOX2B):c.234C>T (p.Tyr78=)

Genes:
PHOX2B-AS1:PHOX2B antisense RNA 1 [Gene - HGNC]
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.234C>T (p.Tyr78=)
HGVS:
  • NC_000004.12:g.41748377G>A
  • NG_008243.1:g.5594C>T
  • NM_003924.4:c.234C>TMANE SELECT
  • NP_003915.2:p.Tyr78=
  • NP_003915.2:p.Tyr78=
  • LRG_513t1:c.234C>T
  • LRG_513:g.5594C>T
  • LRG_513p1:p.Tyr78=
  • NC_000004.11:g.41750394G>A
  • NM_003924.3:c.234C>T
  • p.Tyr78Tyr
Links:
dbSNP: rs73810366
NCBI 1000 Genomes Browser:
rs73810366
Molecular consequence:
  • NM_003924.4:c.234C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000698216Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Benign
(May 17, 2016) 		germlineclinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698216.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

Variant summary: The PHOX2B c.234C>T (p.Tyr78Tyr) variant involves the alteration of a conserved nucleotide, resulting in a synonymous change. MutationTaster predicts a damaging outcome for this variant. 5/5 splice prediction tools predict the variant not to affect normal splicing. This variant was found in 114/120758 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.0101498 (103/10148). This frequency is about 12180 times the estimated maximal expected allele frequency of a pathogenic PHOX2B variant (0.0000008), highly suggesting this is a benign polymorphism found primarily in the populations of African origin. Taken together, this variant is classified as Benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 1, 2024