Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_001379110.1(SLC9A6):c.-57+21del

CA16621203

422694 (ClinVar)

Gene: SLC9A6
Condition: Christianson syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 5cad9377-3823-4bfb-92c5-9fd7ad040f22
Approved on: 2024-02-23
Published on: 2024-03-31

HGVS expressions

NM_001379110.1:c.-57+21del
NM_001379110.1(SLC9A6):c.-57+21del
NC_000023.11:g.135985498del
CM000685.2:g.135985498del
NC_000023.10:g.135067657del
CM000685.1:g.135067657del
NC_000023.9:g.134895323del
NG_017160.1:g.5072del
ENST00000370695.8:c.-5del
ENST00000370701.6:c.-57+21del
ENST00000630721.3:c.-57+21del
ENST00000636092.1:c.-56-105del
ENST00000636347.1:c.-35-126del
ENST00000637195.1:c.-35-126del
ENST00000637234.1:c.-56-105del
ENST00000637581.1:c.-56-105del
ENST00000678163.1:c.-5del
ENST00000370695.6:c.-5del
ENST00000370698.7:c.-5del
ENST00000370701.5:c.-57+21del
ENST00000627534.2:c.-57+26del
NM_001042537.1:c.-5del
NM_001177651.1:c.-57+21del
NM_006359.2:c.-5del
NM_001330652.1:c.-57+26del
NM_001177651.2:c.-57+21del
NM_001330652.2:c.-57+26del
NM_006359.3:c.-5del
NM_001042537.2:c.-5del
NM_001400909.1:c.-35-126del
NM_001400910.1:c.-56-105del
NM_001400911.1:c.-56-105del
NM_001400912.1:c.-57+26del
NM_001400913.1:c.-57+21del
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Benign

Met criteria codes 3
BS2 BS1 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC9A6 Version 3.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The allele frequency of the c.-5del variant in SLC9A6 (NM_006359.2) is 0.02% in European (non-Finnish) sub population in gnomAD v2, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4). The c.-5del variant is observed in the hemizygous state in at least 2 unaffected individuals (internal database - GeneDx) (BS2). In sumarry, the c.-5del variant in SLC9A6 is classified as benign based on the ACMG/AMP criteria (BS1, BP4, BS2).
Met criteria codes
BS2
The c.-5del variant is observed in the hemizygous state in at least 2 unaffected individuals (internal database - GeneDx) (BS2).
BS1
The allele frequency of the c.-5del variant in SLC9A6 (NM_006359.2) is 0.02% in European (non-Finnish) sub population in gnomAD v2, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1).
BP4
Splice prediction analysis, using multiple computational tools does not suggest an impact to splicing (BP4).
Curation History
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