rs2314070
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005629.4(SLC6A8):c.1719G>A(p.Pro573=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000092 in 1,206,758 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 40 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 0.0000089 ( 0 hom., 0 hem., cov: 25)
Exomes 𝑓: 0.00010 ( 0 hom. 40 hem. )
Consequence
SLC6A8
NM_005629.4 synonymous
NM_005629.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.125
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 -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant X-153694841-G-A is Benign according to our data. Variant chrX-153694841-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 379401.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.125 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome4 at 40 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.1719G>A | p.Pro573= | synonymous_variant | 12/13 | ENST00000253122.10 | |
SLC6A8 | NM_001142805.2 | c.1689G>A | p.Pro563= | synonymous_variant | 12/13 | ||
SLC6A8 | NM_001142806.1 | c.1374G>A | p.Pro458= | synonymous_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.1719G>A | p.Pro573= | synonymous_variant | 12/13 | 1 | NM_005629.4 | P1 | |
SLC6A8 | ENST00000430077.6 | c.1374G>A | p.Pro458= | synonymous_variant | 12/13 | 2 | |||
SLC6A8 | ENST00000485324.1 | n.2026G>A | non_coding_transcript_exon_variant | 5/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000886 AC: 1AN: 112928Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35088
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GnomAD3 exomes AF: 0.0000115 AC: 2AN: 174462Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 60918
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GnomAD4 exome AF: 0.000101 AC: 110AN: 1093783Hom.: 0 Cov.: 37 AF XY: 0.000111 AC XY: 40AN XY: 360267
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GnomAD4 genome ? AF: 0.00000885 AC: 1AN: 112975Hom.: 0 Cov.: 25 AF XY: 0.00 AC XY: 0AN XY: 35145
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Creatine transporter deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 25, 2019 | - - |
Computational scores
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Name
Calibrated prediction
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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