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]
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Variant: NM_006359.3(SLC9A6):c.141C>T (p.Gly47=)

CA293620

139211 (ClinVar)

Gene: SLC9A6
Condition: Christianson syndrome
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: f89ea3e7-4808-4b4e-87eb-bfbfdfae5456

HGVS expressions

NM_006359.3:c.141C>T
NM_006359.3(SLC9A6):c.141C>T (p.Gly47=)
NC_000023.11:g.135985643C>T
CM000685.2:g.135985643C>T
NC_000023.10:g.135067802C>T
CM000685.1:g.135067802C>T
NC_000023.9:g.134895468C>T
NG_017160.1:g.5217C>T
ENST00000370695.8:c.141C>T
ENST00000370701.6:c.-16C>T
ENST00000630721.3:c.-16C>T
ENST00000636092.1:c.-16C>T
ENST00000636347.1:c.-16C>T
ENST00000637195.1:c.-16C>T
ENST00000637234.1:c.-16C>T
ENST00000637581.1:c.-16C>T
ENST00000678163.1:c.141C>T
ENST00000370695.6:c.141C>T
ENST00000370698.7:c.141C>T
ENST00000370701.5:c.-16C>T
ENST00000627534.2:c.-16C>T
NM_001042537.1:c.141C>T
NM_001177651.1:c.-16C>T
NM_006359.2:c.141C>T
NM_001330652.1:c.-16C>T
NM_001177651.2:c.-16C>T
NM_001330652.2:c.-16C>T
NM_001042537.2:c.141C>T
NM_001379110.1:c.-16C>T
NM_001400909.1:c.-16C>T
NM_001400910.1:c.-16C>T
NM_001400911.1:c.-16C>T
NM_001400912.1:c.-16C>T
NM_001400913.1:c.-16C>T
NM_001379110.1(SLC9A6):c.-16C>T

Likely Benign

Met criteria codes 2
BS1 BP7

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The allele frequency of the p.Gly47= variant in SLC9A6 is 0.008% in European (Non-Finnish) sub population in gnomAD, 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). The silent p.Gly47= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP7). In summary, the p.Gly47= variant in SLC9A6 is classified as likely benign based on the ACMG/AMP criteria (BS1, BP7).
Met criteria codes
BS1
The allele frequency of the p.Gly47= variant in SLC9A6 is 0.008% in European (Non-Finnish) sub population in gnomAD, which is high enough to be classified as likely benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1).
BP7
The silent p.Gly47= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide.
Approved on: 2022-02-19
Published on: 2022-06-28
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