rs1497020
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000276373.10(SLC18A1):c.*848C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 152,098 control chromosomes in the GnomAD database, including 43,560 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 0.75 ( 43560 hom., cov: 31)
Exomes 𝑓: 0.50 ( 0 hom. )
Consequence
SLC18A1
ENST00000276373.10 3_prime_UTR
ENST00000276373.10 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.759
Genes affected
SLC18A1 (HGNC:10934): (solute carrier family 18 member A1) The vesicular monoamine transporter acts to accumulate cytosolic monoamines into vesicles, using the proton gradient maintained across the vesicular membrane. Its proper function is essential to the correct activity of the monoaminergic systems that have been implicated in several human neuropsychiatric disorders. The transporter is a site of action of important drugs, including reserpine and tetrabenazine (Peter et al., 1993 [PubMed 7905859]). See also SLC18A2 (MIM 193001).[supplied by OMIM, Mar 2008]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC18A1 | NM_003053.4 | c.*848C>T | 3_prime_UTR_variant | 16/16 | ENST00000276373.10 | NP_003044.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC18A1 | ENST00000276373.10 | c.*848C>T | 3_prime_UTR_variant | 16/16 | 1 | NM_003053.4 | ENSP00000276373 | P1 |
Frequencies
GnomAD3 genomes AF: 0.748 AC: 113638AN: 151978Hom.: 43515 Cov.: 31
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GnomAD4 exome AF: 0.500 AC: 1AN: 2Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome AF: 0.748 AC: 113743AN: 152096Hom.: 43560 Cov.: 31 AF XY: 0.743 AC XY: 55192AN XY: 74330
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ClinVar
Not reported inComputational scores
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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