rs782234529
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_005629.4(SLC6A8):c.1768-9C>G variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000142 in 1,197,991 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 6 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_005629.4 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.1768-9C>G | splice_polypyrimidine_tract_variant, intron_variant | ENST00000253122.10 | |||
SLC6A8 | NM_001142805.2 | c.1738-9C>G | splice_polypyrimidine_tract_variant, intron_variant | ||||
SLC6A8 | NM_001142806.1 | c.1423-9C>G | splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.1768-9C>G | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005629.4 | P1 | |||
SLC6A8 | ENST00000430077.6 | c.1423-9C>G | splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
SLC6A8 | ENST00000485324.1 | n.2075-9C>G | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000444 AC: 5AN: 112699Hom.: 0 Cov.: 22 AF XY: 0.0000574 AC XY: 2AN XY: 34849
GnomAD3 exomes AF: 0.0000635 AC: 10AN: 157438Hom.: 0 AF XY: 0.0000818 AC XY: 4AN XY: 48890
GnomAD4 exome AF: 0.0000111 AC: 12AN: 1085240Hom.: 0 Cov.: 31 AF XY: 0.0000113 AC XY: 4AN XY: 354034
GnomAD4 genome ? AF: 0.0000443 AC: 5AN: 112751Hom.: 0 Cov.: 22 AF XY: 0.0000573 AC XY: 2AN XY: 34911
ClinVar
Submissions by phenotype
Creatine transporter deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
SLC6A8-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 11, 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at