rs13241830

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000448817.1(IGFBP3):​c.73+168C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,010 control chromosomes in the GnomAD database, including 6,661 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 0.29 ( 6661 hom., cov: 32)

Consequence

IGFBP3
ENST00000448817.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.132
Variant links:
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=-0.78).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IGFBP3ENST00000448817.1 linkuse as main transcriptc.73+168C>T intron_variant 4 ENSP00000389668

Frequencies

GnomAD3 genomes
AF:
0.288
AC:
43821
AN:
151896
Hom.:
6651
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.278
Gnomad AMI
AF:
0.226
Gnomad AMR
AF:
0.241
Gnomad ASJ
AF:
0.352
Gnomad EAS
AF:
0.0343
Gnomad SAS
AF:
0.332
Gnomad FIN
AF:
0.255
Gnomad MID
AF:
0.345
Gnomad NFE
AF:
0.324
Gnomad OTH
AF:
0.304
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.289
AC:
43873
AN:
152010
Hom.:
6661
Cov.:
32
AF XY:
0.284
AC XY:
21107
AN XY:
74312
show subpopulations
Gnomad4 AFR
AF:
0.278
Gnomad4 AMR
AF:
0.241
Gnomad4 ASJ
AF:
0.352
Gnomad4 EAS
AF:
0.0344
Gnomad4 SAS
AF:
0.334
Gnomad4 FIN
AF:
0.255
Gnomad4 NFE
AF:
0.324
Gnomad4 OTH
AF:
0.311
Alfa
AF:
0.324
Hom.:
1035
Bravo
AF:
0.283
Asia WGS
AF:
0.224
AC:
779
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.78
CADD
Benign
9.7
DANN
Benign
0.93

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13241830; hg19: chr7-45961058; API