X-153688581-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.7A>G(p.Lys3Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000488 in 1,024,037 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. 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 (★). Synonymous variant affecting the same amino acid position (i.e. K3K) has been classified as Likely benign.
Frequency
Consequence
NM_005629.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A8 | NM_005629.4 | c.7A>G | p.Lys3Glu | missense_variant | 1/13 | ENST00000253122.10 | |
SLC6A8 | NM_001142805.2 | c.7A>G | p.Lys3Glu | missense_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A8 | ENST00000253122.10 | c.7A>G | p.Lys3Glu | missense_variant | 1/13 | 1 | NM_005629.4 | P1 | |
PNCK | ENST00000458354.5 | c.-3+234T>C | intron_variant | 3 | |||||
PNCK | ENST00000480693.1 | n.64+234T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000980 AC: 1AN: 102053Hom.: 0 Cov.: 20 AF XY: 0.0000363 AC XY: 1AN XY: 27581
GnomAD4 exome AF: 0.00000434 AC: 4AN: 921984Hom.: 0 Cov.: 22 AF XY: 0.00000347 AC XY: 1AN XY: 288062
GnomAD4 genome ? AF: 0.00000980 AC: 1AN: 102053Hom.: 0 Cov.: 20 AF XY: 0.0000363 AC XY: 1AN XY: 27581
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 23, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports 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