NM_001142805.2:c.1111+37G>A

Version: 1.0
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CA10549426

Gene: SLC6A8 (HGNC:6535)

Condition: creatine transporter deficiency

Inheritance Mode: X-linked inheritance

UUID: 1fd5115f-f240-4cd5-be7d-87fcf5f2dc34

Approved on: 2023-06-08

Published on: 2023-06-08

HGVS expressions

NM_001142805.2:c.1111+37G>A
NC_000023.11:g.153693623G>A
CM000685.2:g.153693623G>A
NC_000023.10:g.152959078G>A
CM000685.1:g.152959078G>A
NC_000023.9:g.152612272G>A
NG_012016.1:g.10327G>A
NG_012016.2:g.10327G>A
ENST00000253122.10:c.1141+37G>A
ENST00000253122.9:c.1141+37G>A
ENST00000413787.1:n.257+37G>A
ENST00000430077.6:c.796+37G>A
ENST00000442457.1:n.195+37G>A
ENST00000457723.1:n.125+37G>A
ENST00000467402.1:n.240+37G>A
ENST00000485324.1:n.1174+37G>A
NM_001142805.1:c.1111+37G>A
NM_001142806.1:c.796+37G>A
NM_005629.3:c.1141+37G>A
NM_005629.4:c.1141+37G>A

Benign

• Met criteria codes: BA1 BP4

Expert Panel

Cerebral Creatine Deficiency Syndromes VCEP

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SLC6A8 Version 1.1.0

Evidence submitted by expert panel

Cerebral Creatine Deficiency Syndromes VCEP

The NM_005629.4:c.1141+37G>A variant is in intron 7 of SLC6A8. The highest population minor allele frequency in gnomAD v2.1.1 is 0.1931 (3670/19008 alleles; 952 hemizygotes and 265 homozygotes) in the African/African American population, which is higher than the ClinGen CCDS VCEP’s threshold for BA1 (>0.002), and therefore meets this criterion (BA1). The computational predictor SpliceAI predicts that the variant has no effect on SLC6A8 splicing (BP4). In summary, this variants meets the criteria to be classified as benign for creatine transporter deficiency. SLC6A8-specific 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 8, 2023)

Met criteria codes

• BA1: The highest population minor allele frequency in gnomAD v2.1.1 is 0.1931 (3670/19008 alleles; 952 hemizygotes and 265 homozygotes) in the African/African American population, which is higher than the ClinGen CCDS VCEP’s threshold for BA1 (>0.002), and therefore meets this criterion (BA1).
• BP4: The computational predictor SpliceAI predicts that the variant has no effect on SLC6A8 splicing (BP4).