rs363223

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003054.6(SLC18A2):​c.992-3683G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,046 control chromosomes in the GnomAD database, including 17,499 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 0.47 ( 17499 hom., cov: 32)

Consequence

SLC18A2
NM_003054.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.657
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]

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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=-0.8).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SLC18A2NM_003054.6 linkuse as main transcriptc.992-3683G>A intron_variant ENST00000644641.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SLC18A2ENST00000644641.2 linkuse as main transcriptc.992-3683G>A intron_variant NM_003054.6 P1Q05940-1
SLC18A2ENST00000497497.1 linkuse as main transcriptn.1408-3683G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.468
AC:
71117
AN:
151928
Hom.:
17501
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.312
Gnomad AMI
AF:
0.629
Gnomad AMR
AF:
0.522
Gnomad ASJ
AF:
0.458
Gnomad EAS
AF:
0.453
Gnomad SAS
AF:
0.496
Gnomad FIN
AF:
0.515
Gnomad MID
AF:
0.370
Gnomad NFE
AF:
0.542
Gnomad OTH
AF:
0.472
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.468
AC:
71131
AN:
152046
Hom.:
17499
Cov.:
32
AF XY:
0.467
AC XY:
34671
AN XY:
74310
show subpopulations
Gnomad4 AFR
AF:
0.312
Gnomad4 AMR
AF:
0.522
Gnomad4 ASJ
AF:
0.458
Gnomad4 EAS
AF:
0.452
Gnomad4 SAS
AF:
0.496
Gnomad4 FIN
AF:
0.515
Gnomad4 NFE
AF:
0.541
Gnomad4 OTH
AF:
0.469
Alfa
AF:
0.407
Hom.:
1692
Bravo
AF:
0.466
Asia WGS
AF:
0.454
AC:
1579
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.80
CADD
Benign
2.1
DANN
Benign
0.54

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs363223; hg19: chr10-119022561; API