rs3863145

Variant names:

• chr5-1392596-G-A
• rs3863145
• NM_001044.5:c.*2139C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-1392596-G-A
• chr5-1392596-G-C
• chr5-1392596-G-T

Variant summary

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

The NM_001044.5(SLC6A3):​c.*2139C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 151,614 control chromosomes in the GnomAD database, including 3,580 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 0.21 (3580 hom., cov: 31)
• Consequence: SLC6A3 NM_001044.5 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.56

Genes affected

SLC6A3 (HGNC:11049): (solute carrier family 6 member 3) This gene encodes a dopamine transporter which is a member of the sodium- and chloride-dependent neurotransmitter transporter family. The 3' UTR of this gene contains a 40 bp tandem repeat, referred to as a variable number tandem repeat or VNTR, which can be present in 3 to 11 copies. Variation in the number of repeats is associated with idiopathic epilepsy, attention-deficit hyperactivity disorder, dependence on alcohol and cocaine, susceptibility to Parkinson disease and protection against nicotine dependence.[provided by RefSeq, Nov 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC6A3	NM_001044.5	c.*2139C>T		downstream_gene_variant		ENST00000270349.12	NP_001035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC6A3	ENST00000270349.12	c.*2139C>T		downstream_gene_variant		1	NM_001044.5	ENSP00000270349.9

Frequencies

GnomAD3 genomes AF: 0.207 AC: 31422 AN: 151498 Hom.: 3581 Cov.: 31

Gnomad AFR AF: 0.130

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.0671

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.207 AC: 31420 AN: 151614 Hom.: 3580 Cov.: 31 AF XY: 0.204 AC XY: 15079 AN XY: 74074

Gnomad4 AFR AF: 0.130

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.0667

Gnomad4 SAS AF: 0.165

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.245

Alfa AF: 0.199 Hom.: 851

Bravo AF: 0.208

Asia WGS AF: 0.110 AC: 382 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.27
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3863145; hg19: chr5-1392711;