Genetic Variant SLC6A3:c.*835_*836insGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGC (chr5-1393899-T-TGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACAC) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001044.5(SLC6A3):c.*835_*836insGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as protective (no stars).

Frequency

Genomes: not found (cov: 30)

Consequence

SLC6A3
NM_001044.5 3_prime_UTR

Scores

Not classified

Clinical Significance

protective no assertion criteria provided B:1

Conservation

PhyloP100: 0.355

Publications

0 publications found

Variant links:

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]

SLC6A3 Gene-Disease associations (from GenCC):

classic dopamine transporter deficiency syndrome
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), G2P, PanelApp Australia, Ambry Genetics
SLC6A3-related dopamine transporter deficiency syndrome
Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
parkinsonism-dystonia, infantile
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

SLC6A3 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001044.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC6A3	NM_001044.5	MANE Select	c.835_836insGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGC		3_prime_UTR	Exon 15 of 15	NP_001035.1	Q01959

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
SLC6A3	ENST00000270349.12	TSL:1 MANE Select	c.835_836insGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGC	3_prime_UTR	Exon 15 of 15	ENSP00000270349.9	Q01959
SLC6A3	ENST00000512002.2	TSL:1	n.129_130insGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGC	downstream_gene	N/A
SLC6A3	ENST00000941790.1		c.835_836insGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGC	downstream_gene	N/A	ENSP00000611849.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:protective

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

Nicotine dependence, protection against (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.35

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over