IGFBP3 p.Ala32Glu

Variant names:

• chr7-45921046-G-T
• rs2854746
• NM_000598.5:c.95C>A
• IGFBP3 p.Ala32Glu

Your query was ambiguous. Multiple possible variants found:

• chr7-45921046-G-T
• chr7-45921045-CG-TT

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

0 Uncertain · Cold

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 0 classification points (ACMG Germline Pathogenicity v2019). PM2BP4_Moderate

The NM_000598.5(IGFBP3):c.95C>A (p.Ala32Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a cumulative frequency of 0.000000775 (AC=1) in the gnomAD database across 1,289,992 control chromosomes (no homozygotes observed). The grpmax filtering allele frequency (95% CI) is 0.000000775. In-silico predictor (REVEL) classifies this variant as likely benign. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.A32V: unknown significance (ClinVar VariationId 4338024)

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.8e-7 (0 hom.)
• Consequence: IGFBP3 NM_000598.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.359
• Publications: 98 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]

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 0 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM2Absent/extremely low in population databases		Very rare in gnomAD for AR/unknown gene (popmax AF < threshold/10) — PM2; GnomAD popmax AF = 0.000000775 — very rare for unknown gene (threshold 0.001) — PM2 moderate.
	BP4Computational evidence suggests no impact		Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); Splicing verdict: benign (Strong).; Germline computational verdict: benign (Moderate).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_000598.5. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	IGFBP3 NM_000598.5	MANE Select	c.95C>A p.Ala32Glu	missense	Exon 1 of 5	Prot: NP_000589.2 UniProt:
	IGFBP3 NM_001013398.2		c.95C>A p.Ala32Glu	missense	Exon 1 of 5	Prot: NP_001013416.1 UniProt:

IGFBP3 NM_000598.5

MANE Select

HGVSc / HGVSpc.95C>Ap.Ala32Glu

Exon rankExon 1 of 5

missense

Prot: NP_000589.2UniProt: P17936-1

IGFBP3 NM_001013398.2

HGVSc / HGVSpc.95C>Ap.Ala32Glu

Exon rankExon 1 of 5

missense

Prot: NP_001013416.1UniProt: P17936-2

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	IGFBP3 ENST00000613132.5	TSL:5MANE Select	c.95C>A p.Ala32Glu	missense	Exon 1 of 5	Prot: ENSP00000477772.2 UniProt:
	IGFBP3 ENST00000908406.1		c.95C>A p.Ala32Glu	missense	Exon 1 of 6	Prot: ENSP00000578465.1 UniProt:
	IGFBP3 ENST00000381083.9	TSL:5	c.95C>A p.Ala32Glu	missense	Exon 1 of 5	Prot: ENSP00000370473.4 UniProt:

IGFBP3 ENST00000613132.5

TSL:5MANE Select

HGVSc / HGVSpc.95C>Ap.Ala32Glu

Exon rankExon 1 of 5

missense

Prot: ENSP00000477772.2UniProt: P17936-1

IGFBP3 ENST00000908406.1

HGVSc / HGVSpc.95C>Ap.Ala32Glu

Exon rankExon 1 of 6

missense

Prot: ENSP00000578465.1UniProt: A0ACI8RUV2

IGFBP3 ENST00000381083.9

TSL:5

HGVSc / HGVSpc.95C>Ap.Ala32Glu

Exon rankExon 1 of 5

missense

Prot: ENSP00000370473.4UniProt: P17936-2

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 5 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:33
GnomAD4 exome	AF: 7.75e-7	AC:1	Hom:0	AN:1289992	Cov:43
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:33
TOPMed (Bravo)	AF: 0.00000378	AC:	Hom:	AN:	Cov:
ALFA (dbGaP/dbSNP Allele Frequency Aggregator)	AF: 0.00	AC:0	Hom:579	AN:15733	Cov:
Local & regional cohorts 2 sources Population-specific and national genomic databases
ABraOM SABE-WGS-1171	AF: 0.00	AC:0	Hom:0	AN:804	Cov:
ToMMo 61KJPN (+60KJPN MNV)	AF: 0.00	AC:0	Hom:0	AN:122448	Cov:

Showing 7 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Benign	8.0
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.30	T
BayesDel_noAF	Benign	-0.66
CADD	Benign	10
DANN	Benign	0.97
DEOGEN2	Benign	0.29	T
Eigen	Benign	-0.62
Eigen_PC	Benign	-0.82
FATHMM_MKL	Benign	0.075	N
FuncVEP CTI	Benign	0.022
GPN-Star LLR	N/A	-5.3
GPN-Star score	N/A	5.3
LIST_S2	Benign	0.49	T
M_CAP	Benign	0.0091	T
MetaRNN	Benign	0.10	T
MetaSVM	Benign	-1.0	T
Mutation Taster	N/A	94/6	polymorphism
MutationAssessor	Benign	0.81	L
PhyloP100	Benign	0.36
popEVE	Benign	-3.0
PrimateAI	Pathogenic	0.87	D
PromoterAI	N/A	-0.061	Neutral
PROVEAN	Benign	-0.44	N
REVEL	Benign	0.058
Sift	Benign	0.27	T
Sift4G	Benign	0.33	T
Varity_R	N/A	0.062
VESM-3B	Benign	-5.1

Showing 29 of 29 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs2854746;

hg19: chr7-45960645;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar