chr17-49036671-T-C

Position:

• chr17-49036671-T-C

Variant summary

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

The ENST00000290341.8(IGF2BP1):​c.402-1497T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.57 in 152,086 control chromosomes in the GnomAD database, including 26,370 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 0.57 (26363 hom., cov: 32)
  • Exomes 𝑓: 0.35 (7 hom.)
• Consequence: IGF2BP1 ENST00000290341.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IGF2BP1	NM_006546.4	c.402-1497T>C		intron_variant		ENST00000290341.8	NP_006537.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IGF2BP1	ENST00000290341.8	c.402-1497T>C		intron_variant		1	NM_006546.4	ENSP00000290341	P1

Frequencies

GnomAD3 genomes AF: 0.570 AC: 86612 AN: 151906 Hom.: 26333 Cov.: 32

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.527

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.516

GnomAD4 exome AF: 0.355 AC: 22 AN: 62 Hom.: 7 Cov.: 0 AF XY: 0.283 AC XY: 13 AN XY: 46

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 NFE exome AF: 0.400

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.570 AC: 86696 AN: 152024 Hom.: 26363 Cov.: 32 AF XY: 0.565 AC XY: 41960 AN XY: 74306

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.527

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.444

Gnomad4 FIN AF: 0.480

Gnomad4 NFE AF: 0.507

Gnomad4 OTH AF: 0.511

Alfa AF: 0.506 Hom.: 19405

Bravo AF: 0.581

Asia WGS AF: 0.366 AC: 1274 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.5
DANN	Benign	0.36

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: rs11870560; hg19: chr17-47114033;