Variant chr10-117254512-C-T details in Genebe, Genetics Data Aggregator

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

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:6

Conservation

PhyloP100: -1.67

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 links:

SLC18A2 (HGNC:):

SLC18A2 links:

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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	Protein	UniProt
SLC18A2	NM_003054.6 linkuse as main transcript	c.700+15C>T		intron_variant		ENST00000644641.2	NP_003045.2	Q05940-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC18A2	ENST00000644641.2 linkuse as main transcript	c.700+15C>T		intron_variant			NM_003054.6	ENSP00000496339.1		Q05940-1
SLC18A2	ENST00000497497.1 linkuse as main transcript	n.1116+15C>T		intron_variant		2

Frequencies

GnomAD3 genomes

AF:

0.895

AC:

136169

AN:

152104

Hom.:

61136

Cov.:

show subpopulations

Gnomad AFR

AF:

0.918

Gnomad AMI

AF:

0.916

Gnomad AMR

AF:

0.899

Gnomad ASJ

AF:

0.896

Gnomad EAS

AF:

0.703

Gnomad SAS

AF:

0.783

Gnomad FIN

AF:

0.925

Gnomad MID

AF:

0.949

Gnomad NFE

AF:

0.898

Gnomad OTH

AF:

0.896

GnomAD3 exomes

AF:

0.877

AC:

195865

AN:

223394

Hom.:

86308

AF XY:

0.875

AC XY:

105050

AN XY:

120050

show subpopulations

Gnomad AFR exome

AF:

0.922

Gnomad AMR exome

AF:

0.887

Gnomad ASJ exome

AF:

0.900

Gnomad EAS exome

AF:

0.700

Gnomad SAS exome

AF:

0.810

Gnomad FIN exome

AF:

0.922

Gnomad NFE exome

AF:

0.902

Gnomad OTH exome

AF:

0.893

GnomAD4 exome

AF:

0.890

AC:

1267011

AN:

1423758

Hom.:

565207

Cov.:

AF XY:

0.888

AC XY:

626760

AN XY:

706126

show subpopulations

Gnomad4 AFR exome

AF:

0.919

Gnomad4 AMR exome

AF:

0.890

Gnomad4 ASJ exome

AF:

0.893

Gnomad4 EAS exome

AF:

0.689

Gnomad4 SAS exome

AF:

0.809

Gnomad4 FIN exome

AF:

0.921

Gnomad4 NFE exome

AF:

0.901

Gnomad4 OTH exome

AF:

0.888

GnomAD4 genome

AF:

0.895

AC:

136268

AN:

152222

Hom.:

61180

Cov.:

AF XY:

0.893

AC XY:

66450

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.918

Gnomad4 AMR

AF:

0.899

Gnomad4 ASJ

AF:

0.896

Gnomad4 EAS

AF:

0.703

Gnomad4 SAS

AF:

0.782

Gnomad4 FIN

AF:

0.925

Gnomad4 NFE

AF:

0.898

Gnomad4 OTH

AF:

0.897

Alfa

AF:

0.895

Hom.:

22627

Bravo

AF:

0.894

Asia WGS

AF:

0.766

AC:

2665

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:6

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -

not specified

Benign:2

Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, Amsterdam University Medical Center	-	- -

Brain dopamine-serotonin vesicular transport disease

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.016

DANN

Benign

0.61

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over