20-63743036-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020062.4(SLC2A4RG):c.*46C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.157 in 1,486,632 control chromosomes in the GnomAD database, including 24,389 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 0.14 ( 2283 hom., cov: 30)
Exomes 𝑓: 0.16 ( 22106 hom. )
Consequence
SLC2A4RG
NM_020062.4 3_prime_UTR
NM_020062.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.152
Genes affected
SLC2A4RG (HGNC:15930): (SLC2A4 regulator) The protein encoded by this gene is a nuclear transcription factor involved in the activation of the solute carrier family 2 member 4 gene. The encoded protein interacts with another transcription factor, myocyte enhancer factor 2, to activate transcription of this gene. [provided by RefSeq, Jul 2008]
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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).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC2A4RG | NM_020062.4 | c.*46C>T | 3_prime_UTR_variant | 8/8 | ENST00000266077.5 | NP_064446.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC2A4RG | ENST00000266077.5 | c.*46C>T | 3_prime_UTR_variant | 8/8 | 1 | NM_020062.4 | ENSP00000266077.2 | |||
SLC2A4RG | ENST00000493772.5 | n.859C>T | non_coding_transcript_exon_variant | 5/5 | 1 | |||||
SLC2A4RG | ENST00000473157.1 | n.522C>T | non_coding_transcript_exon_variant | 5/5 | 3 | |||||
SLC2A4RG | ENST00000496425.1 | n.421C>T | non_coding_transcript_exon_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.136 AC: 20629AN: 151736Hom.: 2281 Cov.: 30
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GnomAD3 exomes AF: 0.209 AC: 30860AN: 147906Hom.: 4669 AF XY: 0.210 AC XY: 16629AN XY: 79058
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GnomAD4 exome AF: 0.160 AC: 213345AN: 1334778Hom.: 22106 Cov.: 21 AF XY: 0.163 AC XY: 106731AN XY: 655142
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GnomAD4 genome AF: 0.136 AC: 20634AN: 151854Hom.: 2283 Cov.: 30 AF XY: 0.141 AC XY: 10476AN XY: 74218
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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