NM_001177316.2(SLC34A3):c.*14A>C AND not provided

Germline classification:: Benign (3 submissions)
Last evaluated:: Aug 30, 2018
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:: RCV000590116.4

Allele description [Variation Report for NM_001177316.2(SLC34A3):c.*14A>C]

NM_001177316.2(SLC34A3):c.*14A>C

Genes:

LOC130003098:ATAC-STARR-seq lymphoblastoid silent region 20596 [Gene]
SLC34A3:solute carrier family 34 member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q34.3

Genomic location:

Preferred name:

NM_001177316.2(SLC34A3):c.*14A>C

HGVS:

NC_000009.12:g.137236430A>C
NG_017008.2:g.10530A>C
NM_001177316.2:c.*14A>CMANE SELECT
NM_001177317.2:c.*14A>C
NM_080877.3:c.*14A>C
NC_000009.11:g.140130882A>C
NM_080877.2:c.*14A>C

Links:

dbSNP: rs28591989

NCBI 1000 Genomes Browser:

rs28591989

Molecular consequence:

NM_001177316.2:c.*14A>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001177317.2:c.*14A>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_080877.3:c.*14A>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

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
SCV000699830	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Benign (Jun 14, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV001935753	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Benign (Aug 30, 2018)	germline	clinical testing	Citation Link,
SCV005318085	Breakthrough Genomics, Breakthrough Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Benign	germline	not provided	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000699830

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Benign
(Jun 14, 2016)

germline

clinical testing

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

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV001935753

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Benign
(Aug 30, 2018)

germline

clinical testing

Citation Link,

SCV005318085

Breakthrough Genomics, Breakthrough Genomics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Benign

germline

not provided

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

Citations

PubMed

Hereditary hypophosphatemic rickets with hypercalciuria is caused by mutations in the sodium-phosphate cotransporter gene SLC34A3.

Lorenz-Depiereux B, Benet-Pages A, Eckstein G, Tenenbaum-Rakover Y, Wagenstaller J, Tiosano D, Gershoni-Baruch R, Albers N, Lichtner P, Schnabel D, Hochberg Z, Strom TM.

Am J Hum Genet. 2006 Feb;78(2):193-201. Epub 2005 Dec 9.

PubMed [citation]

PMID:: 16358215
PMCID:: PMC1380229

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000699830.1

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

Description

Variant summary: The SLC34A3 c.*14A>C variant is located in the 3' UTR at a non-conserved nucleotide. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 7130/17986 (1/2, 1453 homozygotes), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic SLC34A3 variant of 1/894. A reputable clinical laboratory cites the variant as benign. Therefore, taking all available lines of evidence into consideration, the variant of interest is classifed 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, SCV001935753.1

#	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

From Breakthrough Genomics, Breakthrough Genomics, SCV005318085.1

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

#	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: Sep 29, 2024

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