rs1800887
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001172501.3(SLC6A2):c.1590+23T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 1,519,906 control chromosomes in the GnomAD database, including 47,456 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.30 ( 8104 hom., cov: 32)
Exomes 𝑓: 0.23 ( 39352 hom. )
Consequence
SLC6A2
NM_001172501.3 intron
NM_001172501.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.43
Genes affected
SLC6A2 (HGNC:11048): (solute carrier family 6 member 2) This gene encodes a member of the sodium:neurotransmitter symporter family. This member is a multi-pass membrane protein, which is responsible for reuptake of norepinephrine into presynaptic nerve terminals and is a regulator of norepinephrine homeostasis. Mutations in this gene cause orthostatic intolerance, a syndrome characterized by lightheadedness, fatigue, altered mentation and syncope. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene.[provided by RefSeq, Feb 2010]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A2 | NM_001172501.3 | c.1590+23T>C | intron_variant | ENST00000568943.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A2 | ENST00000568943.6 | c.1590+23T>C | intron_variant | 1 | NM_001172501.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.297 AC: 45126AN: 151942Hom.: 8080 Cov.: 32
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GnomAD3 exomes AF: 0.228 AC: 56758AN: 249332Hom.: 7866 AF XY: 0.232 AC XY: 31189AN XY: 134690
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GnomAD4 exome AF: 0.231 AC: 316361AN: 1367846Hom.: 39352 Cov.: 22 AF XY: 0.234 AC XY: 160300AN XY: 685760
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GnomAD4 genome ? AF: 0.297 AC: 45203AN: 152060Hom.: 8104 Cov.: 32 AF XY: 0.299 AC XY: 22213AN XY: 74316
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at