rs12534093
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006547.3(IGF2BP3):c.236+5127A>T variant causes a intron change. The variant allele was found at a frequency of 0.182 in 152,190 control chromosomes in the GnomAD database, including 2,890 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 0.18 ( 2890 hom., cov: 33)
Consequence
IGF2BP3
NM_006547.3 intron
NM_006547.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.65
Genes affected
IGF2BP3 (HGNC:28868): (insulin like growth factor 2 mRNA binding protein 3) The protein encoded by this gene is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. The encoded protein contains several KH domains, which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. A pseudogene exists on chromosome 7, and there are putative pseudogenes on other chromosomes. [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=-0.77).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.289 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGF2BP3 | NM_006547.3 | c.236+5127A>T | intron_variant | ENST00000258729.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGF2BP3 | ENST00000258729.8 | c.236+5127A>T | intron_variant | 1 | NM_006547.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.182 AC: 27736AN: 152072Hom.: 2891 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: 0.182 AC: 27738AN: 152190Hom.: 2890 Cov.: 33 AF XY: 0.181 AC XY: 13435AN XY: 74394
GnomAD4 genome
?
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27738
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152190
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33
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13435
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74394
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504
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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