rs2072362
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_003054.6(SLC18A2):c.700+15C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.89 in 1,575,980 control chromosomes in the GnomAD database, including 626,387 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.90 ( 61180 hom., cov: 32)
Exomes 𝑓: 0.89 ( 565207 hom. )
Consequence
SLC18A2
NM_003054.6 intron
NM_003054.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.67
Genes affected
SLC18A2 (HGNC:10935): (solute carrier family 18 member A2) This gene encodes an transmembrane protein that functions as an ATP-dependent transporter of monoamines, such as dopamine, norepinephrine, serotonin, and histamine. This protein transports amine neurotransmitters into synaptic vesicles. Polymorphisms in this gene may be associated with schizophrenia, bipolar disorder, and other neurological/psychiatric ailments. [provided by RefSeq, Jun 2018]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 10-117254512-C-T is Benign according to our data. Variant chr10-117254512-C-T is described in ClinVar as [Benign]. Clinvar id is 1165075.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-117254512-C-T is described in Lovd as [Benign].
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 | UniProt |
---|---|---|---|---|---|---|---|
SLC18A2 | NM_003054.6 | c.700+15C>T | intron_variant | ENST00000644641.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC18A2 | ENST00000644641.2 | c.700+15C>T | intron_variant | NM_003054.6 | P1 | ||||
SLC18A2 | ENST00000497497.1 | n.1116+15C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.895 AC: 136169AN: 152104Hom.: 61136 Cov.: 32
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GnomAD3 exomes AF: 0.877 AC: 195865AN: 223394Hom.: 86308 AF XY: 0.875 AC XY: 105050AN XY: 120050
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GnomAD4 exome AF: 0.890 AC: 1267011AN: 1423758Hom.: 565207 Cov.: 28 AF XY: 0.888 AC XY: 626760AN XY: 706126
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GnomAD4 genome ? AF: 0.895 AC: 136268AN: 152222Hom.: 61180 Cov.: 32 AF XY: 0.893 AC XY: 66450AN XY: 74426
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ClinVar
Significance: Benign
Submissions summary: Benign:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 15, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Brain dopamine-serotonin vesicular transport disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
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