rs16860216

chr3-185771094-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006548.6(IGF2BP2):c.239+52059C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.295 in 151,946 control chromosomes in the GnomAD database, including 7,192 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 0.30 (7192 hom., cov: 31)
• Consequence: IGF2BP2 NM_006548.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.733

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF2BP2	NM_006548.6	c.239+52059C>T		intron_variant		ENST00000382199.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF2BP2	ENST00000382199.7	c.239+52059C>T		intron_variant		1	NM_006548.6	P1

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44803 AN: 151828 Hom.: 7178 Cov.: 31

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.324

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.268

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.275

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.295 AC: 44852 AN: 151946 Hom.: 7192 Cov.: 31 AF XY: 0.293 AC XY: 21791 AN XY: 74270

Gnomad4 AFR AF: 0.431

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.324

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.273

Alfa AF: 0.246 Hom.: 4692

Bravo AF: 0.293

Asia WGS AF: 0.236 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
Cadd	Benign	6.1
Dann	Benign	0.66
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs16860216; hg19: chr3-185488882;