10-117243797-C-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_003054.6(SLC18A2):c.122-174C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0714 in 152,020 control chromosomes in the GnomAD database, including 580 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.071 (580 hom., cov: 33)
• Consequence: SLC18A2 NM_003054.6 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.589

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]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 10-117243797-C-G is Benign according to our data. Variant chr10-117243797-C-G is described in ClinVar as [Benign]. Clinvar id is 1258075.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC18A2	NM_003054.6	c.122-174C>G		intron_variant		ENST00000644641.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC18A2	ENST00000644641.2	c.122-174C>G		intron_variant			NM_003054.6	P1
SLC18A2	ENST00000497497.1	n.265-174C>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0712 AC: 10822 AN: 151902 Hom.: 574 Cov.: 33

Gnomad AFR AF: 0.0961

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.0340

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.0869

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0714 AC: 10854 AN: 152020 Hom.: 580 Cov.: 33 AF XY: 0.0732 AC XY: 5439 AN XY: 74304

Gnomad4 AFR AF: 0.0965

Gnomad4 AMR AF: 0.160

Gnomad4 ASJ AF: 0.0600

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.0285

Gnomad4 FIN AF: 0.0340

Gnomad4 NFE AF: 0.0415

Gnomad4 OTH AF: 0.0883

Alfa AF: 0.0143 Hom.: 8

Bravo AF: 0.0862

Asia WGS AF: 0.0920 AC: 319 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.1
Dann	Benign	0.69

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

Other links and lift over

dbSNP: rs2240779; hg19: chr10-119003308;