chr2-216636096-A-G

Variant names:

• chr2-216636096-A-G
• rs9341105
• NM_000597.3:c.442+2131A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_000597.3(IGFBP2):​c.442+2131A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.243 in 151,912 control chromosomes in the GnomAD database, including 4,741 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 0.24 (4741 hom., cov: 31)
• Consequence: IGFBP2 NM_000597.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.761
• Publications: 12 publications found

Genes affected

IGFBP2 (HGNC:5471): (insulin like growth factor binding protein 2) The protein encoded by this gene is one of six similar proteins that bind insulin-like growth factors I and II (IGF-I and IGF-II). The encoded protein can be secreted into the bloodstream, where it binds IGF-I and IGF-II with high affinity, or it can remain intracellular, interacting with many different ligands. High expression levels of this protein promote the growth of several types of tumors and may be predictive of the chances of recovery of the patient. Several transcript variants, one encoding a secreted isoform and the others encoding nonsecreted isoforms, have been found for this gene. [provided by RefSeq, Sep 2015]

ENSG00000303260 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGFBP2	NM_000597.3	c.442+2131A>G		intron_variant	Intron 1 of 3	ENST00000233809.9	NP_000588.3
IGFBP2	NM_001313992.2	c.-57+2821A>G		intron_variant	Intron 1 of 3		NP_001300921.1
IGFBP2	NM_001313993.2	c.-57+3082A>G		intron_variant	Intron 1 of 3		NP_001300922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGFBP2	ENST00000233809.9	c.442+2131A>G		intron_variant	Intron 1 of 3	1	NM_000597.3	ENSP00000233809.4
IGFBP2	ENST00000434997.1	c.-57+3082A>G		intron_variant	Intron 1 of 2	3		ENSP00000401698.1
IGFBP2	ENST00000490362.1	n.537+2131A>G		intron_variant	Intron 1 of 1	2
ENSG00000303260	ENST00000793255.1	n.113+239T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.243 AC: 36851 AN: 151794 Hom.: 4738 Cov.: 31

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.320

Gnomad EAS AF: 0.0269

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.252

Gnomad OTH AF: 0.251

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

GnomAD4 genome AF: 0.243 AC: 36859 AN: 151912 Hom.: 4741 Cov.: 31 AF XY: 0.243 AC XY: 18067 AN XY: 74260

African (AFR) AF: 0.248 AC: 10264 AN: 41432

American (AMR) AF: 0.217 AC: 3309 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.320 AC: 1112 AN: 3470

East Asian (EAS) AF: 0.0269 AC: 139 AN: 5160

South Asian (SAS) AF: 0.263 AC: 1260 AN: 4800

European-Finnish (FIN) AF: 0.258 AC: 2726 AN: 10554

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.252 AC: 17091 AN: 67936

Other (OTH) AF: 0.248 AC: 521 AN: 2104

Alfa AF: 0.250 Hom.: 14435

Bravo AF: 0.241

Asia WGS AF: 0.143 AC: 498 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.63
PhyloP100		-0.76
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: rs9341105; hg19: chr2-217500819;