X-153694714-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_005629.4(SLC6A8):c.1597-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,209,202 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. 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 Likely benign (★★).
Frequency
Consequence
NM_005629.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.1597-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000253122.10 | |||
SLC6A8 | NM_001142805.2 | c.1567-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
SLC6A8 | NM_001142806.1 | c.1252-5C>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.1597-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005629.4 | P1 | |||
SLC6A8 | ENST00000430077.6 | c.1252-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
SLC6A8 | ENST00000485324.1 | n.1904-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000712 AC: 8AN: 112419Hom.: 0 Cov.: 25 AF XY: 0.000116 AC XY: 4AN XY: 34615
GnomAD3 exomes AF: 0.000104 AC: 19AN: 182328Hom.: 0 AF XY: 0.0000741 AC XY: 5AN XY: 67492
GnomAD4 exome AF: 0.0000337 AC: 37AN: 1096732Hom.: 0 Cov.: 38 AF XY: 0.0000331 AC XY: 12AN XY: 362796
GnomAD4 genome AF: 0.0000711 AC: 8AN: 112470Hom.: 0 Cov.: 25 AF XY: 0.000115 AC XY: 4AN XY: 34676
ClinVar
Submissions by phenotype
Creatine transporter deficiency Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
SLC6A8-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 04, 2019 | 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). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at