3-76083413-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378191.1(ROBO2):c.109+145811C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.582 in 151,832 control chromosomes in the GnomAD database, including 25,900 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 0.58 (25900 hom., cov: 32)
• Consequence: ROBO2 NM_001378191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.137

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.633 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ROBO2	NM_001128929.3	c.109+145811C>T		intron_variant
ROBO2	NM_001378190.1	c.109+145811C>T		intron_variant
ROBO2	NM_001378191.1	c.109+145811C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ROBO2	ENST00000471893.2	c.109+145811C>T		intron_variant		4
ROBO2	ENST00000487694.7	c.109+145811C>T		intron_variant		5
ROBO2	ENST00000602589.5	c.109+145811C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88277 AN: 151712 Hom.: 25898 Cov.: 32

Gnomad AFR AF: 0.601

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.607

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.582 AC: 88320 AN: 151832 Hom.: 25900 Cov.: 32 AF XY: 0.584 AC XY: 43343 AN XY: 74186

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.390

Gnomad4 SAS AF: 0.652

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.607

Alfa AF: 0.581 Hom.: 4427

Bravo AF: 0.569

Asia WGS AF: 0.568 AC: 1972 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	4.1
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1489100; hg19: chr3-76132564;