17-49051759-G-A

Variant names:

• chr17-49051759-G-A
• rs11655950
• NM_006546.4:c.*2315G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006546.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGF2BP1	NM_006546.4	MANE Select	c.*2315G>A		3_prime_UTR	Exon 15 of 15	NP_006537.3
	IGF2BP1	NM_001160423.2		c.*2315G>A		3_prime_UTR	Exon 13 of 13	NP_001153895.1	Q9NZI8-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IGF2BP1	ENST00000290341.8	TSL:1 MANE Select	c.*2315G>A		3_prime_UTR	Exon 15 of 15	ENSP00000290341.3	Q9NZI8-1
	IGF2BP1	ENST00000925690.1		c.*2315G>A		3_prime_UTR	Exon 15 of 15	ENSP00000595749.1
	IGF2BP1	ENST00000925689.1		c.*2315G>A		3_prime_UTR	Exon 15 of 15	ENSP00000595748.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.418 AC: 17268 AN: 41334

American (AMR) AF: 0.362 AC: 5518 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1396 AN: 3472

East Asian (EAS) AF: 0.0434 AC: 225 AN: 5184

South Asian (SAS) AF: 0.192 AC: 924 AN: 4808

European-Finnish (FIN) AF: 0.291 AC: 3050 AN: 10464

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.322 AC: 21907 AN: 67932

Other (OTH) AF: 0.310 AC: 653 AN: 2104

Alfa AF: 0.317 Hom.: 10447

Bravo AF: 0.345

Asia WGS AF: 0.145 AC: 505 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.73
DANN	Benign	0.85
PhyloP100		-0.47
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: rs11655950; hg19: chr17-47129121;