rs12804553
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000377890.6(SLC3A2):c.298+4486G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 152,244 control chromosomes in the GnomAD database, including 3,909 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 0.21 ( 3909 hom., cov: 33)
Consequence
SLC3A2
ENST00000377890.6 intron
ENST00000377890.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.185
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC3A2 | NM_001012662.3 | c.206-629G>T | intron_variant | ||||
SLC3A2 | NM_001012664.3 | c.113-4864G>T | intron_variant | ||||
SLC3A2 | NM_002394.6 | c.298+4486G>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A2 | ENST00000377889.6 | c.113-4864G>T | intron_variant | 1 | |||||
SLC3A2 | ENST00000377890.6 | c.298+4486G>T | intron_variant | 1 | |||||
SLC3A2 | ENST00000377891.6 | c.206-629G>T | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.207 AC: 31487AN: 152126Hom.: 3905 Cov.: 33
GnomAD3 genomes
?
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.207 AC: 31484AN: 152244Hom.: 3909 Cov.: 33 AF XY: 0.205 AC XY: 15234AN XY: 74426
GnomAD4 genome
?
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33
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15234
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74426
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494
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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