rs187400676
Positions:
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_005629.4(SLC6A8):c.1141+18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00202 in 1,205,279 control chromosomes in the GnomAD database, including 17 homozygotes. There are 758 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0037 ( 3 hom., 164 hem., cov: 24)
Exomes 𝑓: 0.0018 ( 14 hom. 594 hem. )
Consequence
SLC6A8
NM_005629.4 intron
NM_005629.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.95
Genes affected
SLC6A8 (HGNC:11055): (solute carrier family 6 member 8) The protein encoded by this gene is a plasma membrane protein whose function is to transport creatine into and out of cells. Defects in this gene can result in X-linked creatine deficiency syndrome. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant X-153693604-G-A is Benign according to our data. Variant chrX-153693604-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 381457.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-153693604-G-A is described in Lovd as [Likely_benign].
BS1
?
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00374 (422/112828) while in subpopulation AMR AF= 0.031 (333/10738). AF 95% confidence interval is 0.0283. There are 3 homozygotes in gnomad4. There are 164 alleles in male gnomad4 subpopulation. Median coverage is 24. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 3 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.1141+18G>A | intron_variant | ENST00000253122.10 | |||
SLC6A8 | NM_001142805.2 | c.1111+18G>A | intron_variant | ||||
SLC6A8 | NM_001142806.1 | c.796+18G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.1141+18G>A | intron_variant | 1 | NM_005629.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00378 AC: 426AN: 112775Hom.: 3 Cov.: 24 AF XY: 0.00470 AC XY: 164AN XY: 34911
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GnomAD3 exomes AF: 0.00596 AC: 1088AN: 182547Hom.: 9 AF XY: 0.00476 AC XY: 321AN XY: 67487
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GnomAD4 exome AF: 0.00184 AC: 2012AN: 1092451Hom.: 14 Cov.: 31 AF XY: 0.00166 AC XY: 594AN XY: 358591
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GnomAD4 genome ? AF: 0.00374 AC: 422AN: 112828Hom.: 3 Cov.: 24 AF XY: 0.00469 AC XY: 164AN XY: 34974
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 16, 2016 | 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. - |
Creatine transporter deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 20, 2017 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at