rs11655950

Positions:

• chr17-49051759-G-A
• chr17-49051759-G-C
• chr17-49051759-G-T

Variant summary

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

The NM_006546.4(IGF2BP1):​c.*2315G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.338 in 151,760 control chromosomes in the GnomAD database, including 9,202 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 0.34 (9202 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: IGF2BP1 NM_006546.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.467

Genes affected

IGF2BP1 (HGNC:28866): (insulin like growth factor 2 mRNA binding protein 1) This gene encodes a member of the insulin-like growth factor 2 mRNA-binding protein family. The protein encoded by this gene contains four K homology domains and two RNA recognition motifs. It functions by binding to the mRNAs of certain genes, including insulin-like growth factor 2, beta-actin and beta-transducin repeat-containing protein, and regulating their translation. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF2BP1	NM_006546.4	c.*2315G>A		3_prime_UTR_variant	15/15	ENST00000290341.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF2BP1	ENST00000290341.8	c.*2315G>A		3_prime_UTR_variant	15/15	1	NM_006546.4	P1

Frequencies

GnomAD3 genomes AF: 0.338 AC: 51261 AN: 151648 Hom.: 9196 Cov.: 32

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.0435

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.385

Gnomad NFE AF: 0.322

Gnomad OTH AF: 0.313

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.338 AC: 51302 AN: 151760 Hom.: 9202 Cov.: 32 AF XY: 0.334 AC XY: 24796 AN XY: 74144

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.0434

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.322

Gnomad4 OTH AF: 0.310

Alfa AF: 0.309 Hom.: 7669

Bravo AF: 0.345

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.73
DANN	Benign	0.85

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: rs11655950; hg19: chr17-47129121;