rs4304239

Variant names:

• chr7-23456342-G-A
• rs4304239
• NM_006547.3:c.236+12140C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-23456342-G-A
• chr7-23456342-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006547.3(IGF2BP3):​c.236+12140C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,836 control chromosomes in the GnomAD database, including 11,995 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 0.38 (11995 hom., cov: 31)
• Consequence: IGF2BP3 NM_006547.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.573
• Publications: 9 publications found

Genes affected

IGF2BP3 (HGNC:28868): (insulin like growth factor 2 mRNA binding protein 3) The protein encoded by this gene is primarily found in the nucleolus, where it can bind to the 5' UTR of the insulin-like growth factor II leader 3 mRNA and may repress translation of insulin-like growth factor II during late development. The encoded protein contains several KH domains, which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. A pseudogene exists on chromosome 7, and there are putative pseudogenes on other chromosomes. [provided by RefSeq, Jul 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGF2BP3	NM_006547.3	c.236+12140C>T		intron_variant	Intron 2 of 14	ENST00000258729.8	NP_006538.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGF2BP3	ENST00000258729.8	c.236+12140C>T		intron_variant	Intron 2 of 14	1	NM_006547.3	ENSP00000258729.3

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58111 AN: 151722 Hom.: 11973 Cov.: 31

Gnomad AFR AF: 0.519

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.0522

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.373

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.383 AC: 58180 AN: 151836 Hom.: 11995 Cov.: 31 AF XY: 0.373 AC XY: 27692 AN XY: 74242

African (AFR) AF: 0.519 AC: 21495 AN: 41380

American (AMR) AF: 0.307 AC: 4680 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1099 AN: 3472

East Asian (EAS) AF: 0.0524 AC: 270 AN: 5156

South Asian (SAS) AF: 0.332 AC: 1601 AN: 4824

European-Finnish (FIN) AF: 0.248 AC: 2612 AN: 10524

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.373 AC: 25347 AN: 67938

Other (OTH) AF: 0.394 AC: 830 AN: 2106

Alfa AF: 0.374 Hom.: 46328

Bravo AF: 0.389

Asia WGS AF: 0.212 AC: 742 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.54
DANN	Benign	0.34
PhyloP100		-0.57
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

Other links and lift over

dbSNP: rs4304239; hg19: chr7-23495961;