ClinVar Miner

Submissions for variant NM_005629.4(SLC6A8):c.1016+9C>T

gnomAD frequency: 0.00047  dbSNP: rs190690083
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen RCV000467082 SCV002600189 benign Creatine transporter deficiency 2022-06-06 reviewed by expert panel curation 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).
GeneDx RCV000424385 SCV000516295 likely benign not specified 2018-01-03 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000467082 SCV000561170 benign Creatine transporter deficiency 2024-01-21 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003922726 SCV004739473 likely benign SLC6A8-related condition 2019-05-22 criteria provided, single submitter clinical testing 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).

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