Variant chr5-1393899-T-TGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACAC details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6

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. 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

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 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant 5-1393899-T-TGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACAC is Benign according to our data. Variant chr5-1393899-T-TGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACACGCTCCTGTGGGGGCCCTGCATGCGTCCGGGGATAGGACAC is described in ClinVar as [protective]. Clinvar id is 16762.Status of the report is no_assertion_criteria_provided, 0 stars. We mark this variant Likely_benign, oryginal submission is: [protective].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC6A3	NM_001044.5 linkuse as main transcript	c.835_836insGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGC		3_prime_UTR_variant	15/15	ENST00000270349.12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC6A3	ENST00000270349.12 linkuse as main transcript	c.835_836insGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGCGTGTCCTATCCCCGGACGCATGCAGGGCCCCCACAGGAGC		3_prime_UTR_variant	15/15	1	NM_001044.5	P1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Significance: protective

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Nicotine dependence, protection against

Benign:1

protective, no assertion criteria provided

literature only

OMIM

Jan 01, 1999

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over