rs6351
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001044.5(SLC6A3):c.162C>T(p.Pro54=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0103 in 1,614,186 control chromosomes in the GnomAD database, including 111 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P54P) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A3 | NM_001044.5 | c.162C>T | p.Pro54= | synonymous_variant | 2/15 | ENST00000270349.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A3 | ENST00000270349.12 | c.162C>T | p.Pro54= | synonymous_variant | 2/15 | 1 | NM_001044.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00639 AC: 972AN: 152178Hom.: 6 Cov.: 33
GnomAD3 exomes AF: 0.00704 AC: 1769AN: 251378Hom.: 13 AF XY: 0.00761 AC XY: 1034AN XY: 135900
GnomAD4 exome AF: 0.0107 AC: 15663AN: 1461890Hom.: 105 Cov.: 33 AF XY: 0.0107 AC XY: 7772AN XY: 727244
GnomAD4 genome ? AF: 0.00638 AC: 971AN: 152296Hom.: 6 Cov.: 33 AF XY: 0.00611 AC XY: 455AN XY: 74478
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2020 | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | SLC6A3: BP4, BP7, BS1, BS2 - |
Classic dopamine transporter deficiency syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | Jun 28, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Parkinsonism-dystonia, infantile Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at