GeneBe

NM_003054.6:c.45C>T

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7

The NM_003054.6(SLC18A2):​c.45C>T​(p.Ser15Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000687 in 1,456,600 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)
Exomes 𝑓: 6.9e-7 ( 0 hom. )

Consequence

SLC18A2
NM_003054.6 synonymous

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.00

Publications

0 publications found
Variant links:
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]
SLC18A2-AS1 (HGNC:55843): (SLC18A2 antisense RNA 1)

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.28).
BP7
Synonymous conserved (PhyloP=1 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SLC18A2NM_003054.6 linkc.45C>T p.Ser15Ser synonymous_variant Exon 2 of 16 ENST00000644641.2 NP_003045.2 Q05940-1
SLC18A2-AS1NR_184310.1 linkn.159G>A non_coding_transcript_exon_variant Exon 2 of 3
SLC18A2-AS1NR_184309.1 linkn.113+147G>A intron_variant Intron 1 of 1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SLC18A2ENST00000644641.2 linkc.45C>T p.Ser15Ser synonymous_variant Exon 2 of 16 NM_003054.6 ENSP00000496339.1 Q05940-1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
6.87e-7
AC:
1
AN:
1456600
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
724348
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
33184
American (AMR)
AF:
0.00
AC:
0
AN:
44502
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25972
East Asian (EAS)
AF:
0.00
AC:
0
AN:
39376
South Asian (SAS)
AF:
0.00
AC:
0
AN:
85706
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
51936
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
5392
European-Non Finnish (NFE)
AF:
9.01e-7
AC:
1
AN:
1110412
Other (OTH)
AF:
0.00
AC:
0
AN:
60120
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.28
CADD
Benign
17
DANN
Benign
0.97
PhyloP100
1.0
Mutation Taster
=100/0
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs371946127; hg19: chr10-119001249; API