rs6876225

Positions:

• chr5-1405921-C-A
• chr5-1405921-C-T

Variant summary

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

The NM_001044.5(SLC6A3):​c.1599+267G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 152,270 control chromosomes in the GnomAD database, including 694 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.085 (694 hom., cov: 33)
• Consequence: SLC6A3 NM_001044.5 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -2.01

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 5-1405921-C-A is Benign according to our data. Variant chr5-1405921-C-A is described in ClinVar as [Benign]. Clinvar id is 1272852.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC6A3	NM_001044.5	c.1599+267G>T		intron_variant		ENST00000270349.12	NP_001035.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SLC6A3	ENST00000270349.12	c.1599+267G>T		intron_variant		1	NM_001044.5	ENSP00000270349	P1

Frequencies

GnomAD3 genomes AF: 0.0847 AC: 12891 AN: 152152 Hom.: 693 Cov.: 33

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0406

Gnomad ASJ AF: 0.0462

Gnomad EAS AF: 0.0120

Gnomad SAS AF: 0.0653

Gnomad FIN AF: 0.0781

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0635

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0848 AC: 12912 AN: 152270 Hom.: 694 Cov.: 33 AF XY: 0.0829 AC XY: 6172 AN XY: 74464

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.0405

Gnomad4 ASJ AF: 0.0462

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.0657

Gnomad4 FIN AF: 0.0781

Gnomad4 NFE AF: 0.0635

Gnomad4 OTH AF: 0.0644

Alfa AF: 0.0455 Hom.: 56

Bravo AF: 0.0838

Asia WGS AF: 0.0360 AC: 124 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

Aug 17, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.097
DANN	Benign	0.29

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: rs6876225; hg19: chr5-1406036;