rs16830101
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006516.4(SLC2A1):c.114+327G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0981 in 385,920 control chromosomes in the GnomAD database, including 2,208 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 0.090 ( 783 hom., cov: 31)
Exomes 𝑓: 0.10 ( 1425 hom. )
Consequence
SLC2A1
NM_006516.4 intron
NM_006516.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.781
Genes affected
SLC2A1 (HGNC:11005): (solute carrier family 2 member 1) This gene encodes a major glucose transporter in the mammalian blood-brain barrier. The encoded protein is found primarily in the cell membrane and on the cell surface, where it can also function as a receptor for human T-cell leukemia virus (HTLV) I and II. Mutations in this gene have been found in a family with paroxysmal exertion-induced dyskinesia. [provided by RefSeq, Apr 2013]
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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=-0.81).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC2A1 | NM_006516.4 | c.114+327G>C | intron_variant | ENST00000426263.10 | NP_006507.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC2A1 | ENST00000426263.10 | c.114+327G>C | intron_variant | 1 | NM_006516.4 | ENSP00000416293 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0900 AC: 13687AN: 152032Hom.: 780 Cov.: 31
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GnomAD4 exome AF: 0.103 AC: 24137AN: 233770Hom.: 1425 AF XY: 0.107 AC XY: 13445AN XY: 125912
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GnomAD4 genome AF: 0.0901 AC: 13706AN: 152150Hom.: 783 Cov.: 31 AF XY: 0.0928 AC XY: 6902AN XY: 74364
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at