X-153688582-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005629.4(SLC6A8):c.8A>G(p.Lys3Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005629.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.8A>G | p.Lys3Arg | missense_variant | Exon 1 of 13 | 1 | NM_005629.4 | ENSP00000253122.5 | ||
PNCK | ENST00000458354.5 | c.-3+233T>C | intron_variant | Intron 1 of 3 | 3 | ENSP00000401542.1 | ||||
PNCK | ENST00000480693.1 | n.64+233T>C | intron_variant | Intron 1 of 3 | 5 | |||||
SLC6A8 | ENST00000476466.1 | n.-141A>G | upstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 20
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000109 AC: 1AN: 921450Hom.: 0 Cov.: 22 AF XY: 0.00000348 AC XY: 1AN XY: 287438
GnomAD4 genome Cov.: 20
ClinVar
Submissions by phenotype
not provided Uncertain:1
Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at