chr3-185813873-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006548.6(IGF2BP2):​c.239+9280G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0951 in 152,238 control chromosomes in the GnomAD database, including 827 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 0.095 ( 827 hom., cov: 32)

Consequence

IGF2BP2
NM_006548.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.483

Publications

26 publications found
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]
IGF2BP2 Gene-Disease associations (from GenCC):
  • diabetes mellitus, noninsulin-dependent
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: Labcorp Genetics (formerly Invitae)

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IGF2BP2NM_006548.6 linkc.239+9280G>A intron_variant Intron 2 of 15 ENST00000382199.7 NP_006539.3 Q9Y6M1-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IGF2BP2ENST00000382199.7 linkc.239+9280G>A intron_variant Intron 2 of 15 1 NM_006548.6 ENSP00000371634.3 Q9Y6M1-2

Frequencies

GnomAD3 genomes
AF:
0.0949
AC:
14432
AN:
152120
Hom.:
820
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.161
Gnomad AMI
AF:
0.0910
Gnomad AMR
AF:
0.100
Gnomad ASJ
AF:
0.0824
Gnomad EAS
AF:
0.0932
Gnomad SAS
AF:
0.158
Gnomad FIN
AF:
0.0199
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.0615
Gnomad OTH
AF:
0.0863
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0951
AC:
14471
AN:
152238
Hom.:
827
Cov.:
32
AF XY:
0.0939
AC XY:
6988
AN XY:
74438
show subpopulations
African (AFR)
AF:
0.162
AC:
6712
AN:
41508
American (AMR)
AF:
0.100
AC:
1537
AN:
15298
Ashkenazi Jewish (ASJ)
AF:
0.0824
AC:
286
AN:
3470
East Asian (EAS)
AF:
0.0934
AC:
484
AN:
5182
South Asian (SAS)
AF:
0.158
AC:
761
AN:
4822
European-Finnish (FIN)
AF:
0.0199
AC:
211
AN:
10612
Middle Eastern (MID)
AF:
0.102
AC:
30
AN:
294
European-Non Finnish (NFE)
AF:
0.0615
AC:
4181
AN:
68032
Other (OTH)
AF:
0.0882
AC:
186
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
667
1335
2002
2670
3337
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
170
340
510
680
850
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0761
Hom.:
1134
Bravo
AF:
0.0999
Asia WGS
AF:
0.142
AC:
492
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.51
CADD
Benign
16
DANN
Benign
0.87
PhyloP100
0.48
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1
Mutation Taster
=100/0
polymorphism (auto)

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

Other links and lift over

dbSNP: rs1374910; hg19: chr3-185531661; API