rs2854747
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000598.5(IGFBP3):c.403+420C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 192,158 control chromosomes in the GnomAD database, including 33,418 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 0.59 ( 26248 hom., cov: 31)
Exomes 𝑓: 0.58 ( 7170 hom. )
Consequence
IGFBP3
NM_000598.5 intron
NM_000598.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.407
Genes affected
IGFBP3 (HGNC:5472): (insulin like growth factor binding protein 3) This gene is a member of the insulin-like growth factor binding protein (IGFBP) family and encodes a protein with an IGFBP domain and a thyroglobulin type-I domain. The protein forms a ternary complex with insulin-like growth factor acid-labile subunit (IGFALS) and either insulin-like growth factor (IGF) I or II. In this form, it circulates in the plasma, prolonging the half-life of IGFs and altering their interaction with cell surface receptors. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [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=-0.81).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.74 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGFBP3 | NM_000598.5 | c.403+420C>T | intron_variant | ENST00000613132.5 | |||
IGFBP3 | NM_001013398.2 | c.421+402C>T | intron_variant | ||||
IGFBP3 | XM_047420325.1 | c.403+420C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGFBP3 | ENST00000613132.5 | c.403+420C>T | intron_variant | 5 | NM_000598.5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.587 AC: 88727AN: 151104Hom.: 26245 Cov.: 31
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GnomAD4 exome AF: 0.582 AC: 23820AN: 40938Hom.: 7170 Cov.: 0 AF XY: 0.583 AC XY: 11989AN XY: 20560
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GnomAD4 genome ? AF: 0.587 AC: 88763AN: 151220Hom.: 26248 Cov.: 31 AF XY: 0.581 AC XY: 42847AN XY: 73802
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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