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GeneBe

rs4402960

chr3-185793899-G-Cchr3-185793899-G-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The NM_006548(IGF2BP2):c.239+29254C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0 ( 0 hom., cov: 29)
Failed GnomAD Quality Control

Consequence

IGF2BP2
NM_006548 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.107

Links

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IGF2BP2NM_006548.6 linkuse as main transcriptc.239+29254C>G intron_variant ENST00000382199.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IGF2BP2ENST00000382199.7 linkuse as main transcriptc.239+29254C>G intron_variant 1 NM_006548.6 P1Q9Y6M1-2

Frequencies

GnomAD3 genomes
AF:
0.00
AC:
0
AN:
150950
Hom.:
0
Cov.:
29
FAILED QC
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
Cadd
Benign
1.0
Dann
Benign
0.54

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs4402960; hg19: chr3-185511687;