rs2937639
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001044.5(SLC6A3):c.-45-371A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 152,170 control chromosomes in the GnomAD database, including 19,976 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.50 ( 19976 hom., cov: 33)
Consequence
SLC6A3
NM_001044.5 intron
NM_001044.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.519
Publications
23 publications found
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]
SLC6A3 Gene-Disease associations (from GenCC):
- classic dopamine transporter deficiency syndromeInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, G2P
- SLC6A3-related dopamine transporter deficiency syndromeInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- parkinsonism-dystonia, infantileInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC6A3 | ENST00000270349.12 | c.-45-371A>G | intron_variant | Intron 1 of 14 | 1 | NM_001044.5 | ENSP00000270349.9 | |||
SLC6A3 | ENST00000713696.1 | c.-45-371A>G | intron_variant | Intron 1 of 14 | ENSP00000519000.1 | |||||
SLC6A3 | ENST00000713698.1 | c.-45-371A>G | intron_variant | Intron 1 of 4 | ENSP00000519002.1 | |||||
SLC6A3 | ENST00000713697.1 | n.-45-371A>G | intron_variant | Intron 1 of 10 | ENSP00000519001.1 |
Frequencies
GnomAD3 genomes AF: 0.498 AC: 75721AN: 152050Hom.: 19959 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
75721
AN:
152050
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.498 AC: 75783AN: 152170Hom.: 19976 Cov.: 33 AF XY: 0.496 AC XY: 36913AN XY: 74394 show subpopulations
GnomAD4 genome
AF:
AC:
75783
AN:
152170
Hom.:
Cov.:
33
AF XY:
AC XY:
36913
AN XY:
74394
show subpopulations
African (AFR)
AF:
AC:
14914
AN:
41496
American (AMR)
AF:
AC:
7339
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
2098
AN:
3470
East Asian (EAS)
AF:
AC:
904
AN:
5182
South Asian (SAS)
AF:
AC:
2408
AN:
4824
European-Finnish (FIN)
AF:
AC:
5907
AN:
10582
Middle Eastern (MID)
AF:
AC:
168
AN:
294
European-Non Finnish (NFE)
AF:
AC:
40367
AN:
67996
Other (OTH)
AF:
AC:
1100
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1888
3776
5664
7552
9440
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
682
1364
2046
2728
3410
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1239
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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