rs6670
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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.*1195A>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 0.183 in 152,606 control chromosomes in the GnomAD database, including 2,946 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 ( 2937 hom., cov: 32)
Exomes 𝑓: 0.16 ( 9 hom. )
Consequence
IGFBP3
NM_000598.5 3_prime_UTR
NM_000598.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.146
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 (SAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IGFBP3 | NM_000598.5 | c.*1195A>T | 3_prime_UTR_variant | 5/5 | ENST00000613132.5 | ||
IGFBP3 | NM_001013398.2 | c.*1195A>T | 3_prime_UTR_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGFBP3 | ENST00000613132.5 | c.*1195A>T | 3_prime_UTR_variant | 5/5 | 5 | NM_000598.5 | P4 | ||
IGFBP3 | ENST00000381083.9 | c.*1195A>T | 3_prime_UTR_variant | 5/5 | 5 | A1 | |||
IGFBP3 | ENST00000381086.9 | c.*1195A>T | 3_prime_UTR_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.183 AC: 27877AN: 152050Hom.: 2938 Cov.: 32
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GnomAD4 exome AF: 0.162 AC: 71AN: 438Hom.: 9 Cov.: 0 AF XY: 0.173 AC XY: 46AN XY: 266
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GnomAD4 genome ? AF: 0.183 AC: 27882AN: 152168Hom.: 2937 Cov.: 32 AF XY: 0.183 AC XY: 13579AN XY: 74374
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at