chr16-55657912-C-CTCCTGCGGTGCTCAG
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001172501.3(SLC6A2):c.274+950_274+951insGGTGCTCAGTCCTGC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000099 ( 0 hom., cov: 0)
Consequence
SLC6A2
NM_001172501.3 intron
NM_001172501.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0720
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 Likely_benign. Variant got -4 ACMG points.
BS2
?
High AC in GnomAd at 15 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC6A2 | NM_001172501.3 | c.274+950_274+951insGGTGCTCAGTCCTGC | intron_variant | ENST00000568943.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC6A2 | ENST00000568943.6 | c.274+950_274+951insGGTGCTCAGTCCTGC | intron_variant | 1 | NM_001172501.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000988 AC: 15AN: 151798Hom.: 0 Cov.: 0
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GnomAD4 genome ? AF: 0.0000988 AC: 15AN: 151798Hom.: 0 Cov.: 0 AF XY: 0.000135 AC XY: 10AN XY: 74098
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ClinVar
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at