rs13120371
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_014331.4(SLC7A11):c.*391T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 183,130 control chromosomes in the GnomAD database, including 9,066 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 0.29 ( 7228 hom., cov: 31)
Exomes 𝑓: 0.33 ( 1838 hom. )
Consequence
SLC7A11
NM_014331.4 3_prime_UTR
NM_014331.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.701
Genes affected
SLC7A11 (HGNC:11059): (solute carrier family 7 member 11) This gene encodes a member of a heteromeric, sodium-independent, anionic amino acid transport system that is highly specific for cysteine and glutamate. In this system, designated Xc(-), the anionic form of cysteine is transported in exchange for glutamate. This protein has been identified as the predominant mediator of Kaposi sarcoma-associated herpesvirus fusion and entry permissiveness into cells. Also, increased expression of this gene in primary gliomas (compared to normal brain tissue) was associated with increased glutamate secretion via the XCT channels, resulting in neuronal cell death. [provided by RefSeq, Sep 2011]
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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=-0.84).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.365 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC7A11 | NM_014331.4 | c.*391T>C | 3_prime_UTR_variant | 12/12 | ENST00000280612.9 | NP_055146.1 | ||
SLC7A11 | XM_047449957.1 | c.*391T>C | 3_prime_UTR_variant | 18/18 | XP_047305913.1 | |||
SLC7A11-AS1 | NR_038380.1 | n.1860A>G | non_coding_transcript_exon_variant | 5/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC7A11 | ENST00000280612.9 | c.*391T>C | 3_prime_UTR_variant | 12/12 | 1 | NM_014331.4 | ENSP00000280612.5 | |||
SLC7A11-AS1 | ENST00000510767.5 | n.1860A>G | non_coding_transcript_exon_variant | 5/7 | 1 | |||||
SLC7A11-AS1 | ENST00000512786.1 | n.584+2747A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.292 AC: 44316AN: 151928Hom.: 7235 Cov.: 31
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GnomAD4 exome AF: 0.335 AC: 10413AN: 31084Hom.: 1838 Cov.: 0 AF XY: 0.338 AC XY: 5260AN XY: 15558
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GnomAD4 genome AF: 0.291 AC: 44310AN: 152046Hom.: 7228 Cov.: 31 AF XY: 0.297 AC XY: 22081AN XY: 74314
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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
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at