17-48996587-T-C

Position:

• chr17-48996587-T-C

Variant summary

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

The XM_047435139.1(IGF2BP1):​c.-763T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.647 in 152,272 control chromosomes in the GnomAD database, including 32,620 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 0.65 (32582 hom., cov: 32)
  • Exomes 𝑓: 0.61 (38 hom.)
• Consequence: IGF2BP1 XM_047435139.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

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]

ENSG00000250838 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGF2BP1	XM_047435139.1	c.-763T>C		5_prime_UTR_variant	1/16		XP_047291095.1
IGF2BP1	XM_011524201.3	c.-536T>C		5_prime_UTR_variant	1/17		XP_011522503.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000250838	ENST00000505903.1	n.38-96A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98236 AN: 151958 Hom.: 32527 Cov.: 32

Gnomad AFR AF: 0.801

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.572

Gnomad EAS AF: 0.657

Gnomad SAS AF: 0.565

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.615

GnomAD4 exome AF: 0.607 AC: 119 AN: 196 Hom.: 38 AF XY: 0.592 AC XY: 84 AN XY: 142

Gnomad4 AMR exome AF: 1.00

Gnomad4 EAS exome AF: 0.833

Gnomad4 FIN exome AF: 0.462

Gnomad4 NFE exome AF: 0.610

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.647 AC: 98354 AN: 152076 Hom.: 32582 Cov.: 32 AF XY: 0.644 AC XY: 47908 AN XY: 74344

Gnomad4 AFR AF: 0.801

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.572

Gnomad4 EAS AF: 0.656

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.573

Gnomad4 NFE AF: 0.577

Gnomad4 OTH AF: 0.618

Alfa AF: 0.543 Hom.: 4513

Bravo AF: 0.657

Asia WGS AF: 0.652 AC: 2269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	12
DANN	Benign	0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9890278; hg19: chr17-47073949;