chrX-153694529-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005629.4(SLC6A8):c.1496-4G>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 23)
Consequence
SLC6A8
NM_005629.4 splice_region, splice_polypyrimidine_tract, intron
NM_005629.4 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0003029
2
Clinical Significance
Conservation
PhyloP100: -3.71
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 Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.1496-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000253122.10 | |||
SLC6A8 | NM_001142805.2 | c.1466-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SLC6A8 | NM_001142806.1 | c.1151-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.1496-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005629.4 | P1 | |||
SLC6A8 | ENST00000413787.1 | c.425-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
SLC6A8 | ENST00000430077.6 | c.1151-4G>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
SLC6A8 | ENST00000485324.1 | n.1799G>T | non_coding_transcript_exon_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD3 genomes
?
Cov.:
23
GnomAD4 exome Cov.: 34
GnomAD4 exome
Cov.:
34
GnomAD4 genome ? Cov.: 23
GnomAD4 genome
?
Cov.:
23
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 11, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at