rs10082463

Positions:

• chr10-117261896-A-C
• chr10-117261896-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003054.6(SLC18A2):​c.991+4004A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,126 control chromosomes in the GnomAD database, including 1,541 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 0.13 (1541 hom., cov: 33)
• Consequence: SLC18A2 NM_003054.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.80

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC18A2	NM_003054.6	c.991+4004A>C		intron_variant		ENST00000644641.2	NP_003045.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC18A2	ENST00000644641.2	c.991+4004A>C		intron_variant			NM_003054.6	ENSP00000496339	P1
SLC18A2	ENST00000497497.1	n.1407+4004A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19353 AN: 152006 Hom.: 1538 Cov.: 33

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.136

Gnomad EAS AF: 0.396

Gnomad SAS AF: 0.178

Gnomad FIN AF: 0.0527

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.0954

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.127 AC: 19376 AN: 152126 Hom.: 1541 Cov.: 33 AF XY: 0.131 AC XY: 9738 AN XY: 74356

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.136

Gnomad4 EAS AF: 0.397

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.0527

Gnomad4 NFE AF: 0.0954

Gnomad4 OTH AF: 0.127

Alfa AF: 0.102 Hom.: 1291

Bravo AF: 0.139

Asia WGS AF: 0.274 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.16
DANN	Benign	0.45

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: rs10082463; hg19: chr10-119021407;