rs12274689
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000377890.6(SLC3A2):c.299-226C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00703 in 825,818 control chromosomes in the GnomAD database, including 263 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 0.026 ( 179 hom., cov: 32)
Exomes 𝑓: 0.0028 ( 84 hom. )
Consequence
SLC3A2
ENST00000377890.6 intron
ENST00000377890.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.411
Genes affected
SLC3A2 (HGNC:11026): (solute carrier family 3 member 2) This gene is a member of the solute carrier family and encodes a cell surface, transmembrane protein. The protein exists as the heavy chain of a heterodimer, covalently bound through di-sulfide bonds to one of several possible light chains. The encoded transporter plays a role in regulation of intracellular calcium levels and transports L-type amino acids. Alternatively spliced transcript variants, encoding different isoforms, have been characterized. [provided by RefSeq, Nov 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=-0.77).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0878 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC3A2 | NM_001012662.3 | c.302-226C>G | intron_variant | ||||
SLC3A2 | NM_001012664.3 | c.113-226C>G | intron_variant | ||||
SLC3A2 | NM_002394.6 | c.299-226C>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A2 | ENST00000377889.6 | c.113-226C>G | intron_variant | 1 | |||||
SLC3A2 | ENST00000377890.6 | c.299-226C>G | intron_variant | 1 | |||||
SLC3A2 | ENST00000377891.6 | c.302-226C>G | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0257 AC: 3909AN: 152242Hom.: 179 Cov.: 32
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GnomAD4 exome AF: 0.00280 AC: 1889AN: 673458Hom.: 84 Cov.: 9 AF XY: 0.00231 AC XY: 781AN XY: 338400
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GnomAD4 genome AF: 0.0257 AC: 3919AN: 152360Hom.: 179 Cov.: 32 AF XY: 0.0254 AC XY: 1890AN XY: 74510
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at