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NM_001379110.1(SLC9A6):c.-60T>C AND SLC9A6-related disorder

Germline classification:
Likely benign (1 submission)
Last evaluated:
Jan 29, 2021
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV003970124.2

Allele description [Variation Report for NM_001379110.1(SLC9A6):c.-60T>C]

NM_001379110.1(SLC9A6):c.-60T>C

Genes:
LOC130068746:ATAC-STARR-seq lymphoblastoid silent region 21025 [Gene]
SLC9A6:solute carrier family 9 member A6 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq26.3
Genomic location:
Preferred name:
NM_001379110.1(SLC9A6):c.-60T>C
HGVS:
  • NC_000023.11:g.135985474T>C
  • NG_017160.1:g.5048T>C
  • NG_017160.2:g.16639T>C
  • NM_001042537.2:c.-29T>C
  • NM_001177651.2:c.-60T>C
  • NM_001330652.1:c.-57+2T>C
  • NM_001330652.2:c.-57+2T>C
  • NM_001379110.1:c.-60T>CMANE SELECT
  • NM_001400909.1:c.-35-150T>C
  • NM_001400910.1:c.-56-129T>C
  • NM_001400911.1:c.-56-129T>C
  • NM_001400912.1:c.-57+2T>C
  • NM_001400913.1:c.-60T>C
  • NM_006359.3:c.-29T>C
  • NC_000023.10:g.135067633T>C
  • NM_006359.2:c.-29T>C
Links:
dbSNP: rs1057520373
NCBI 1000 Genomes Browser:
rs1057520373
Molecular consequence:
  • NM_001042537.2:c.-29T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001177651.2:c.-60T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001379110.1:c.-60T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001400913.1:c.-60T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_006359.3:c.-29T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001400909.1:c.-35-150T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001400910.1:c.-56-129T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001400911.1:c.-56-129T>C - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001330652.2:c.-57+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001400912.1:c.-57+2T>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:
SLC9A6-related disorder
Synonyms:
SLC9A6-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004785782PreventionGenetics, part of Exact Sciences
no assertion criteria provided
Likely benign
(Jan 29, 2021) 		germlineclinical testing

Help

Summary from all submissions

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

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004785782.2

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

Description

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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

Last Updated: Oct 13, 2024