chr5-1394545-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001044.5(SLC6A3):c.*190C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00625 in 703,522 control chromosomes in the GnomAD database, including 56 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0097 ( 25 hom., cov: 33)
Exomes 𝑓: 0.0053 ( 31 hom. )
Consequence
SLC6A3
NM_001044.5 3_prime_UTR
NM_001044.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.0280
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
?
Variant 5-1394545-G-A is Benign according to our data. Variant chr5-1394545-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1197770.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00969 (1476/152344) while in subpopulation AFR AF= 0.0259 (1076/41572). AF 95% confidence interval is 0.0246. There are 25 homozygotes in gnomad4. There are 763 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 25 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A3 | NM_001044.5 | c.*190C>T | 3_prime_UTR_variant | 15/15 | ENST00000270349.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A3 | ENST00000270349.12 | c.*190C>T | 3_prime_UTR_variant | 15/15 | 1 | NM_001044.5 | P1 | ||
SLC6A3 | ENST00000512002.2 | n.434C>T | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00961 AC: 1463AN: 152226Hom.: 25 Cov.: 33
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GnomAD4 exome AF: 0.00530 AC: 2920AN: 551178Hom.: 31 Cov.: 5 AF XY: 0.00561 AC XY: 1662AN XY: 296346
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GnomAD4 genome ? AF: 0.00969 AC: 1476AN: 152344Hom.: 25 Cov.: 33 AF XY: 0.0102 AC XY: 763AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 27, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at