chr7-45920349-T-TC

Variant names:

• chr7-45920349-T-TC
• rs11292609
• NM_000598.5:c.403+388dupG

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000598.5(IGFBP3):​c.403+388dupG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: IGFBP3 NM_000598.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 0 publications found

Genes affected

IGFBP3 (HGNC:5472): (insulin like growth factor binding protein 3) This gene is a member of the insulin-like growth factor binding protein (IGFBP) family and encodes a protein with an IGFBP domain and a thyroglobulin type-I domain. The protein forms a ternary complex with insulin-like growth factor acid-labile subunit (IGFALS) and either insulin-like growth factor (IGF) I or II. In this form, it circulates in the plasma, prolonging the half-life of IGFs and altering their interaction with cell surface receptors. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IGFBP3	NM_000598.5	c.403+388dupG		intron_variant	Intron 1 of 4	ENST00000613132.5	NP_000589.2
IGFBP3	NM_001013398.2	c.421+370dupG		intron_variant	Intron 1 of 4		NP_001013416.1
IGFBP3	XM_047420325.1	c.403+388dupG		intron_variant	Intron 1 of 3		XP_047276281.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IGFBP3	ENST00000613132.5	c.403+388dupG		intron_variant	Intron 1 of 4	5	NM_000598.5	ENSP00000477772.2

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 68668 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 34466

African (AFR) AF: 0.00 AC: 0 AN: 2686

American (AMR) AF: 0.00 AC: 0 AN: 1932

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2884

East Asian (EAS) AF: 0.00 AC: 0 AN: 5416

South Asian (SAS) AF: 0.00 AC: 0 AN: 652

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4424

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 422

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 45370

Other (OTH) AF: 0.00 AC: 0 AN: 4882

GnomAD4 genome Cov.: 0

Alfa AF: 0.00 Hom.: 2214

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.14

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: rs11292609; hg19: chr7-45959948;