rs1403848

Variant summary

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

The NM_001395656.1(ROBO2):​c.1450-2147C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.609 in 151,912 control chromosomes in the GnomAD database, including 28,643 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 0.61 ( 28643 hom., cov: 32)

Consequence

ROBO2
NM_001395656.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.346
Variant links:
Genes affected
ROBO2 (HGNC:10250): (roundabout guidance receptor 2) The protein encoded by this gene belongs to the ROBO family, part of the immunoglobulin superfamily of proteins that are highly conserved from fly to human. The encoded protein is a transmembrane receptor for the slit homolog 2 protein and functions in axon guidance and cell migration. Mutations in this gene are associated with vesicoureteral reflux, characterized by the backward flow of urine from the bladder into the ureters or the kidney. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

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=-1.0).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ROBO2NM_001395656.1 linkuse as main transcriptc.1450-2147C>A intron_variant ENST00000696593.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ROBO2ENST00000696593.1 linkuse as main transcriptc.1450-2147C>A intron_variant NM_001395656.1 A2

Frequencies

GnomAD3 genomes
AF:
0.609
AC:
92479
AN:
151794
Hom.:
28616
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.705
Gnomad AMI
AF:
0.570
Gnomad AMR
AF:
0.645
Gnomad ASJ
AF:
0.662
Gnomad EAS
AF:
0.653
Gnomad SAS
AF:
0.612
Gnomad FIN
AF:
0.499
Gnomad MID
AF:
0.696
Gnomad NFE
AF:
0.553
Gnomad OTH
AF:
0.639
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.609
AC:
92560
AN:
151912
Hom.:
28643
Cov.:
32
AF XY:
0.610
AC XY:
45244
AN XY:
74230
show subpopulations
Gnomad4 AFR
AF:
0.705
Gnomad4 AMR
AF:
0.645
Gnomad4 ASJ
AF:
0.662
Gnomad4 EAS
AF:
0.654
Gnomad4 SAS
AF:
0.612
Gnomad4 FIN
AF:
0.499
Gnomad4 NFE
AF:
0.553
Gnomad4 OTH
AF:
0.640
Alfa
AF:
0.570
Hom.:
11499
Bravo
AF:
0.625
Asia WGS
AF:
0.661
AC:
2298
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.0
CADD
Benign
1.3
DANN
Benign
0.49

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

Publications

LitVar

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

Other links and lift over

dbSNP: rs1403848; hg19: chr3-77609655; API