10-117241804-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_003054.6(SLC18A2):c.111C>T(p.Leu37=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Consequence
SLC18A2
NM_003054.6 synonymous
NM_003054.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.257
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 Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.37).
BP6
?
Variant 10-117241804-C-T is Benign according to our data. Variant chr10-117241804-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 743190.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.257 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC18A2 | NM_003054.6 | c.111C>T | p.Leu37= | synonymous_variant | 2/16 | ENST00000644641.2 | |
SLC18A2-AS1 | NR_184309.1 | n.113+81G>A | intron_variant, non_coding_transcript_variant | ||||
SLC18A2-AS1 | NR_184310.1 | n.114-21G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC18A2 | ENST00000644641.2 | c.111C>T | p.Leu37= | synonymous_variant | 2/16 | NM_003054.6 | P1 | ||
SLC18A2-AS1 | ENST00000425264.2 | n.115-21G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
SLC18A2 | ENST00000497497.1 | n.254C>T | non_coding_transcript_exon_variant | 2/15 | 2 | ||||
SLC18A2-AS1 | ENST00000691914.2 | n.113+81G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 04, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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