rs775748

Variant summary

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

The NM_001395656.1(ROBO2):​c.1071+847T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,922 control chromosomes in the GnomAD database, including 22,388 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 0.54 ( 22388 hom., cov: 32)

Consequence

ROBO2
NM_001395656.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00700
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=-0.85).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ROBO2NM_001395656.1 linkuse as main transcriptc.1071+847T>A intron_variant ENST00000696593.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ROBO2ENST00000696593.1 linkuse as main transcriptc.1071+847T>A intron_variant NM_001395656.1 A2

Frequencies

GnomAD3 genomes
AF:
0.542
AC:
82289
AN:
151806
Hom.:
22390
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.521
Gnomad AMI
AF:
0.570
Gnomad AMR
AF:
0.583
Gnomad ASJ
AF:
0.676
Gnomad EAS
AF:
0.522
Gnomad SAS
AF:
0.563
Gnomad FIN
AF:
0.495
Gnomad MID
AF:
0.684
Gnomad NFE
AF:
0.544
Gnomad OTH
AF:
0.582
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.542
AC:
82306
AN:
151922
Hom.:
22388
Cov.:
32
AF XY:
0.543
AC XY:
40331
AN XY:
74246
show subpopulations
Gnomad4 AFR
AF:
0.521
Gnomad4 AMR
AF:
0.583
Gnomad4 ASJ
AF:
0.676
Gnomad4 EAS
AF:
0.522
Gnomad4 SAS
AF:
0.563
Gnomad4 FIN
AF:
0.495
Gnomad4 NFE
AF:
0.544
Gnomad4 OTH
AF:
0.579
Alfa
AF:
0.532
Hom.:
2695
Bravo
AF:
0.549
Asia WGS
AF:
0.534
AC:
1861
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
0.85
DANN
Benign
0.36

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: rs775748; hg19: chr3-77596460; API