rs6346
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001044.5(SLC6A3):c.150G>T(p.Pro50=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00779 in 1,614,162 control chromosomes in the GnomAD database, including 842 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. P50P) has been classified as Likely benign.
Frequency
Consequence
NM_001044.5 synonymous
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 |
---|---|---|---|---|---|---|---|
SLC6A3 | NM_001044.5 | c.150G>T | p.Pro50= | synonymous_variant | 2/15 | ENST00000270349.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A3 | ENST00000270349.12 | c.150G>T | p.Pro50= | synonymous_variant | 2/15 | 1 | NM_001044.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0403 AC: 6138AN: 152158Hom.: 452 Cov.: 33
GnomAD3 exomes AF: 0.0110 AC: 2773AN: 251404Hom.: 161 AF XY: 0.00816 AC XY: 1109AN XY: 135902
GnomAD4 exome AF: 0.00438 AC: 6406AN: 1461886Hom.: 387 Cov.: 33 AF XY: 0.00380 AC XY: 2764AN XY: 727242
GnomAD4 genome AF: 0.0405 AC: 6164AN: 152276Hom.: 455 Cov.: 33 AF XY: 0.0391 AC XY: 2915AN XY: 74458
ClinVar
Submissions by phenotype
Parkinsonism-dystonia, infantile Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 17, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at