NM_033409.4(SLC52A3):c.9C>T (p.Phe3=) AND not specified

Germline classification:: Benign (1 submission)
Last evaluated:: Aug 23, 2017
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:: RCV000246921.11

Allele description [Variation Report for NM_033409.4(SLC52A3):c.9C>T (p.Phe3=)]

NM_033409.4(SLC52A3):c.9C>T (p.Phe3=)

Gene:

SLC52A3:solute carrier family 52 member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

20p13

Genomic location:

Preferred name:

NM_033409.4(SLC52A3):c.9C>T (p.Phe3=)

HGVS:

NC_000020.11:g.765766G>A
NG_027687.2:g.15220C>T
NM_001370085.1:c.9C>T
NM_001370086.1:c.9C>T
NM_033409.4:c.9C>TMANE SELECT
NP_001357014.1:p.Phe3=
NP_001357015.1:p.Phe3=
NP_212134.3:p.Phe3=
LRG_1394t1:c.9C>T
LRG_1394:g.15220C>T
LRG_1394p1:p.Phe3=
NC_000020.10:g.746410G>A
NG_027687.1:g.7819C>T
NM_033409.3:c.9C>T
p.Phe3Phe

Links:

dbSNP: rs139486822

NCBI 1000 Genomes Browser:

rs139486822

Molecular consequence:

NM_001370085.1:c.9C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001370086.1:c.9C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_033409.4:c.9C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000713605	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Benign (Aug 23, 2017)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000713605

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Benign
(Aug 23, 2017)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	4	4	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000713605.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	4	not provided	not provided	clinical testing	PubMed (1)

Description

p.Phe3Phe in exon 2 of SLC52A3: This variant is not expected to have clinical si gnificance because it does not alter an amino acid residue, is not located withi n the splice consensus sequence, and has been identified in 0.94% (566/60078) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.bro adinstitute.org; dbSNP rs139486822).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		4	not provided	4	not provided

Last Updated: Oct 20, 2024

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