17-49003069-G-T

Position:

• chr17-49003069-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.236+3900G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.587 in 151,978 control chromosomes in the GnomAD database, including 27,640 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 0.59 (27640 hom., cov: 31)
• Consequence: IGF2BP1 NM_006546.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

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]

LOC124904020 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.768 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IGF2BP1	NM_006546.4	c.236+3900G>T		intron_variant		ENST00000290341.8
LOC124904020	XR_007065831.1	n.2184C>A		non_coding_transcript_exon_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IGF2BP1	ENST00000290341.8	c.236+3900G>T		intron_variant		1	NM_006546.4	P1
IGF2BP1	ENST00000431824.2	c.236+3900G>T		intron_variant		1
IGF2BP1	ENST00000510023.5	n.497-1532G>T		intron_variant, non_coding_transcript_variant		3
IGF2BP1	ENST00000515586.5	n.219+3900G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.587 AC: 89102 AN: 151860 Hom.: 27594 Cov.: 31

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.539

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.587 AC: 89208 AN: 151978 Hom.: 27640 Cov.: 31 AF XY: 0.580 AC XY: 43082 AN XY: 74278

Gnomad4 AFR AF: 0.775

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.215

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.539

Gnomad4 OTH AF: 0.540

Alfa AF: 0.553 Hom.: 7090

Bravo AF: 0.597

Asia WGS AF: 0.369 AC: 1287 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	9.3
DANN	Benign	0.34

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: rs1994969; hg19: chr17-47080431;