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_005629.4(SLC6A8):c.1016+9C>T

CA10549374

379398 (ClinVar)

Gene: SLC6A8
Condition: creatine transporter deficiency
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 971c5d4c-e8e2-40e4-99d7-74db21549e54
Approved on: 2022-06-06
Published on: 2022-10-08

HGVS expressions

NM_005629.4:c.1016+9C>T
NM_005629.4(SLC6A8):c.1016+9C>T
NC_000023.11:g.153693375C>T
CM000685.2:g.153693375C>T
NC_000023.10:g.152958830C>T
CM000685.1:g.152958830C>T
NC_000023.9:g.152612024C>T
NG_012016.1:g.10079C>T
NG_012016.2:g.10079C>T
ENST00000253122.10:c.1016+9C>T
ENST00000253122.9:c.1016+9C>T
ENST00000413787.1:n.162+9C>T
ENST00000430077.6:c.671+9C>T
ENST00000442457.1:n.100+9C>T
ENST00000467402.1:n.146-117C>T
ENST00000485324.1:n.1049+9C>T
NM_001142805.1:c.1016+9C>T
NM_001142806.1:c.671+9C>T
NM_005629.3:c.1016+9C>T
NM_001142805.2:c.1016+9C>T
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Benign

Met criteria codes 2
BA1 BP4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC6A8 Version 1

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_005629.4:c.1016+9C>T variant in SLC6A8 is an intronic variant in the region of the donor splice site of intron 6. The total number of hemizygotes in gnomAD v2.1.1 is 46, meeting the ClinGen CCDS VCEP’s threshold for BA1 (>10 hemizygotes). The highest minor allele frequency is 0.0009212 (European non-Finnish) with 39 hemizygotes in that population (BA1). The computational predictors SpliceAI and varSEAK predict that the variant has no impact in splicing (BP4). There is a ClinVar entry for the variant (Variation ID: 379398). In summary, this variant meets the criteria to be classified as benign for creatine transporter deficiency. SLC6A8-specific ACMG-AMP criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0): BA1, BP4. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).
Met criteria codes
BA1
The total number of hemizygotes in gnomAD v2.1.1 is 46, meeting the ClinGen CCDS VCEP’s threshold for BA1 (>10 hemizygotes). The highest minor allele frequency is 0.0009212 (European non-Finnish) with 39 hemizygotes in that population (BA1).
BP4
The computational predictors SpliceAI and varSEAK predict that the variant has no impact in splicing (BP4).
Curation History
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