rs8076005
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001045.6(SLC6A4):c.344-1261C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,070 control chromosomes in the GnomAD database, including 39,279 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 0.69 ( 39279 hom., cov: 32)
Consequence
SLC6A4
NM_001045.6 intron
NM_001045.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.301
Genes affected
SLC6A4 (HGNC:11050): (solute carrier family 6 member 4) This gene encodes an integral membrane protein that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The encoded protein terminates the action of serotonin and recycles it in a sodium-dependent manner. This protein is a target of psychomotor stimulants, such as amphetamines and cocaine, and is a member of the sodium:neurotransmitter symporter family. A repeat length polymorphism in the promoter of this gene has been shown to affect the rate of serotonin uptake. There have been conflicting results in the literature about the possible effect, if any, that this polymorphism may play in behavior and depression. [provided by RefSeq, May 2019]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A4 | NM_001045.6 | c.344-1261C>T | intron_variant | ENST00000650711.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A4 | ENST00000650711.1 | c.344-1261C>T | intron_variant | NM_001045.6 | P1 | ||||
SLC6A4 | ENST00000261707.7 | c.344-1261C>T | intron_variant | 1 | P1 | ||||
SLC6A4 | ENST00000394821.2 | c.344-1261C>T | intron_variant | 1 | |||||
SLC6A4 | ENST00000401766.6 | c.344-1261C>T | intron_variant | 5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.690 AC: 104814AN: 151952Hom.: 39263 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.690 AC: 104854AN: 152070Hom.: 39279 Cov.: 32 AF XY: 0.695 AC XY: 51681AN XY: 74338
GnomAD4 genome
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2804
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
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