rs6349
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Variant summary
Our verdict is Benign. Variant got -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBA1
The NM_001044.5(SLC6A3):c.1731C>T(p.Ala577=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0085 in 1,614,000 control chromosomes in the GnomAD database, including 354 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.028 ( 154 hom., cov: 32)
Exomes 𝑓: 0.0065 ( 200 hom. )
Consequence
SLC6A3
NM_001044.5 synonymous
NM_001044.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 3.04
Genes affected
SLC6A3 (HGNC:11049): (solute carrier family 6 member 3) This gene encodes a dopamine transporter which is a member of the sodium- and chloride-dependent neurotransmitter transporter family. The 3' UTR of this gene contains a 40 bp tandem repeat, referred to as a variable number tandem repeat or VNTR, which can be present in 3 to 11 copies. Variation in the number of repeats is associated with idiopathic epilepsy, attention-deficit hyperactivity disorder, dependence on alcohol and cocaine, susceptibility to Parkinson disease and protection against nicotine dependence.[provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -18 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 5-1402958-G-A is Benign according to our data. Variant chr5-1402958-G-A is described in ClinVar as [Benign]. Clinvar id is 287682.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-1402958-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0807 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A3 | NM_001044.5 | c.1731C>T | p.Ala577= | synonymous_variant | 13/15 | ENST00000270349.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A3 | ENST00000270349.12 | c.1731C>T | p.Ala577= | synonymous_variant | 13/15 | 1 | NM_001044.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0275 AC: 4182AN: 152184Hom.: 155 Cov.: 32
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GnomAD3 exomes AF: 0.0124 AC: 3116AN: 250924Hom.: 80 AF XY: 0.0110 AC XY: 1491AN XY: 135792
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GnomAD4 exome AF: 0.00652 AC: 9532AN: 1461698Hom.: 200 Cov.: 33 AF XY: 0.00658 AC XY: 4781AN XY: 727140
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GnomAD4 genome ? AF: 0.0275 AC: 4189AN: 152302Hom.: 154 Cov.: 32 AF XY: 0.0264 AC XY: 1966AN XY: 74486
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Apr 21, 2016 | - - |
Parkinsonism-dystonia, infantile Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 26, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 17, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
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DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at