chr5-1394500-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001044.5(SLC6A3):c.*235G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00293 in 634,504 control chromosomes in the GnomAD database, including 25 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0087 ( 20 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 5 hom. )
Consequence
SLC6A3
NM_001044.5 3_prime_UTR
NM_001044.5 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.941
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=-0.77).
BP6
?
Variant 5-1394500-C-T is Benign according to our data. Variant chr5-1394500-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1215152.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00866 (1318/152278) while in subpopulation AFR AF= 0.0295 (1224/41546). AF 95% confidence interval is 0.0281. There are 20 homozygotes in gnomad4. There are 606 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 20 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A3 | NM_001044.5 | c.*235G>A | 3_prime_UTR_variant | 15/15 | ENST00000270349.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A3 | ENST00000270349.12 | c.*235G>A | 3_prime_UTR_variant | 15/15 | 1 | NM_001044.5 | P1 | ||
SLC6A3 | ENST00000512002.2 | n.479G>A | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00864 AC: 1315AN: 152160Hom.: 20 Cov.: 33
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GnomAD4 exome AF: 0.00113 AC: 544AN: 482226Hom.: 5 Cov.: 3 AF XY: 0.000949 AC XY: 243AN XY: 256140
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GnomAD4 genome ? AF: 0.00866 AC: 1318AN: 152278Hom.: 20 Cov.: 33 AF XY: 0.00814 AC XY: 606AN XY: 74454
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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 | Aug 17, 2018 | - - |
Computational scores
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Benign
Cadd
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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