Variant chr10-117277114-T-C 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.1441-48T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.108 in 1,077,238 control chromosomes in the GnomAD database, including 8,199 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 1143 hom., cov: 32)

Exomes 𝑓: 0.11 ( 7056 hom. )

Consequence

SLC18A2
NM_003054.6 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.127

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:

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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=-0.82).

BP6

Variant 10-117277114-T-C is Benign according to our data. Variant chr10-117277114-T-C is described in ClinVar as [Benign]. Clinvar id is 1283694.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.328 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.1441-48T>C		intron_variant		ENST00000644641.2	NP_003045.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC18A2	ENST00000644641.2 linkuse as main transcript	c.1441-48T>C		intron_variant			NM_003054.6	ENSP00000496339	P1	Q05940-1
SLC18A2	ENST00000497497.1 linkuse as main transcript	n.1857-48T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes

AF:

0.106

AC:

16088

AN:

152144

Hom.:

1140

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0848

Gnomad AMI

AF:

0.0330

Gnomad AMR

AF:

0.181

Gnomad ASJ

AF:

0.116

Gnomad EAS

AF:

0.341

Gnomad SAS

AF:

0.166

Gnomad FIN

AF:

0.0503

Gnomad MID

AF:

0.171

Gnomad NFE

AF:

0.0879

Gnomad OTH

AF:

0.113

GnomAD3 exomes

AF:

0.130

AC:

26649

AN:

205080

Hom.:

2382

AF XY:

0.128

AC XY:

14216

AN XY:

111250

show subpopulations

Gnomad AFR exome

AF:

0.0847

Gnomad AMR exome

AF:

0.217

Gnomad ASJ exome

AF:

0.124

Gnomad EAS exome

AF:

0.352

Gnomad SAS exome

AF:

0.158

Gnomad FIN exome

AF:

0.0532

Gnomad NFE exome

AF:

0.0888

Gnomad OTH exome

AF:

0.127

GnomAD4 exome

AF:

0.108

AC:

99844

AN:

924976

Hom.:

7056

Cov.:

AF XY:

0.109

AC XY:

52299

AN XY:

479904

show subpopulations

Gnomad4 AFR exome

AF:

0.0839

Gnomad4 AMR exome

AF:

0.202

Gnomad4 ASJ exome

AF:

0.121

Gnomad4 EAS exome

AF:

0.342

Gnomad4 SAS exome

AF:

0.157

Gnomad4 FIN exome

AF:

0.0552

Gnomad4 NFE exome

AF:

0.0883

Gnomad4 OTH exome

AF:

0.120

GnomAD4 genome

AF:

0.106

AC:

16101

AN:

152262

Hom.:

1143

Cov.:

AF XY:

0.110

AC XY:

8181

AN XY:

74454

show subpopulations

Gnomad4 AFR

AF:

0.0847

Gnomad4 AMR

AF:

0.182

Gnomad4 ASJ

AF:

0.116

Gnomad4 EAS

AF:

0.341

Gnomad4 SAS

AF:

0.167

Gnomad4 FIN

AF:

0.0503

Gnomad4 NFE

AF:

0.0879

Gnomad4 OTH

AF:

0.112

Alfa

AF:

0.0961

Hom.:

207

Bravo

AF:

0.115

Asia WGS

AF:

0.249

AC:

866

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 14, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.6

DANN

Benign

0.81

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