rs9869293

Variant summary

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

The NM_006548.6(IGF2BP2):​c.239+11879T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0438 in 152,268 control chromosomes in the GnomAD database, including 468 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 0.044 ( 468 hom., cov: 32)

Consequence

IGF2BP2
NM_006548.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.733
Variant links:
Genes affected
IGF2BP2 (HGNC:28867): (insulin like growth factor 2 mRNA binding protein 2) This gene encodes a protein that binds the 5' UTR of insulin-like growth factor 2 (IGF2) mRNA and regulates its translation. It plays an important role in metabolism and variation in this gene is associated with susceptibility to diabetes. Alternative splicing and promoter usage results in multiple transcript variants. Related pseudogenes are found on several chromosomes. [provided by RefSeq, Sep 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IGF2BP2NM_006548.6 linkuse as main transcriptc.239+11879T>C intron_variant ENST00000382199.7 NP_006539.3 Q9Y6M1-2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IGF2BP2ENST00000382199.7 linkuse as main transcriptc.239+11879T>C intron_variant 1 NM_006548.6 ENSP00000371634.3 Q9Y6M1-2

Frequencies

GnomAD3 genomes
AF:
0.0437
AC:
6642
AN:
152150
Hom.:
467
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.151
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0186
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00145
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.000779
Gnomad OTH
AF:
0.0306
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0438
AC:
6665
AN:
152268
Hom.:
468
Cov.:
32
AF XY:
0.0414
AC XY:
3086
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.151
Gnomad4 AMR
AF:
0.0188
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00145
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000779
Gnomad4 OTH
AF:
0.0307
Alfa
AF:
0.00783
Hom.:
70
Bravo
AF:
0.0500
Asia WGS
AF:
0.0100
AC:
35
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
5.2
DANN
Benign
0.82

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs9869293; hg19: chr3-185529062; API