rs7126772
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000377890.6(SLC3A2):c.299-491A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0106 in 153,078 control chromosomes in the GnomAD database, including 20 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 0.011 ( 20 hom., cov: 32)
Exomes 𝑓: 0.0012 ( 0 hom. )
Consequence
SLC3A2
ENST00000377890.6 intron
ENST00000377890.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.36
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=-0.85).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0106 (1617/152240) while in subpopulation AFR AF= 0.0368 (1527/41526). AF 95% confidence interval is 0.0352. There are 20 homozygotes in gnomad4. There are 735 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1618 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC3A2 | NM_001012662.3 | c.302-491A>G | intron_variant | ||||
SLC3A2 | NM_001012664.3 | c.113-491A>G | intron_variant | ||||
SLC3A2 | NM_002394.6 | c.299-491A>G | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC3A2 | ENST00000377889.6 | c.113-491A>G | intron_variant | 1 | |||||
SLC3A2 | ENST00000377890.6 | c.299-491A>G | intron_variant | 1 | |||||
SLC3A2 | ENST00000544377.2 | c.-78A>G | 5_prime_UTR_variant | 1/10 | 4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0106 AC: 1618AN: 152122Hom.: 20 Cov.: 32
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GnomAD4 exome AF: 0.00119 AC: 1AN: 838Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 512
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GnomAD4 genome ? AF: 0.0106 AC: 1617AN: 152240Hom.: 20 Cov.: 32 AF XY: 0.00987 AC XY: 735AN XY: 74440
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3478
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