rs13015993

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_187138.1(IGFBP-AS1):​n.407-4089G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.644 in 151,986 control chromosomes in the GnomAD database, including 32,360 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 0.64 ( 32360 hom., cov: 32)

Consequence

IGFBP-AS1
NR_187138.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.563
Variant links:
Genes affected
IGFBP-AS1 (HGNC:55655): (IGFBP5 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
IGFBP-AS1NR_187138.1 linkn.407-4089G>A intron_variant
IGFBP-AS1NR_187139.1 linkn.407-4089G>A intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DIRC3-AS1ENST00000447289.1 linkn.389-4089G>A intron_variant 5
DIRC3-AS1ENST00000695932.1 linkn.448+48331G>A intron_variant
DIRC3-AS1ENST00000695934.1 linkn.111+48331G>A intron_variant
DIRC3-AS1ENST00000702642.1 linkn.324-38749G>A intron_variant

Frequencies

GnomAD3 genomes
AF:
0.644
AC:
97873
AN:
151866
Hom.:
32340
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.508
Gnomad AMI
AF:
0.703
Gnomad AMR
AF:
0.621
Gnomad ASJ
AF:
0.758
Gnomad EAS
AF:
0.522
Gnomad SAS
AF:
0.702
Gnomad FIN
AF:
0.625
Gnomad MID
AF:
0.726
Gnomad NFE
AF:
0.733
Gnomad OTH
AF:
0.683
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.644
AC:
97928
AN:
151986
Hom.:
32360
Cov.:
32
AF XY:
0.640
AC XY:
47501
AN XY:
74262
show subpopulations
Gnomad4 AFR
AF:
0.508
Gnomad4 AMR
AF:
0.621
Gnomad4 ASJ
AF:
0.758
Gnomad4 EAS
AF:
0.522
Gnomad4 SAS
AF:
0.703
Gnomad4 FIN
AF:
0.625
Gnomad4 NFE
AF:
0.733
Gnomad4 OTH
AF:
0.688
Alfa
AF:
0.716
Hom.:
63875
Bravo
AF:
0.637
Asia WGS
AF:
0.652
AC:
2269
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
2.0
DANN
Benign
0.52

Splicing

Find out detailed SpliceAI scores 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: rs13015993; hg19: chr2-217625523; API