rs16860234

chr3-185793096-A-C

Variant summary

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

The NM_006548.6(IGF2BP2):c.239+30057T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 152,070 control chromosomes in the GnomAD database, including 8,488 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 0.32 (8488 hom., cov: 32)
• Consequence: IGF2BP2 NM_006548.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.349

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF2BP2	NM_006548.6	c.239+30057T>G		intron_variant		ENST00000382199.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF2BP2	ENST00000382199.7	c.239+30057T>G		intron_variant		1	NM_006548.6	P1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49180 AN: 151952 Hom.: 8478 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.248

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.324 AC: 49229 AN: 152070 Hom.: 8488 Cov.: 32 AF XY: 0.322 AC XY: 23949 AN XY: 74346

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.374

Gnomad4 EAS AF: 0.168

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.302

Gnomad4 NFE AF: 0.283

Gnomad4 OTH AF: 0.306

Alfa AF: 0.284 Hom.: 10938

Bravo AF: 0.319

Asia WGS AF: 0.305 AC: 1058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.2
Dann	Benign	0.34

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: rs16860234; hg19: chr3-185510884; COSMIC: COSV60492229;