rs13322362

Positions:

• chr3-76481656-C-T

Variant summary

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

The NM_001394212.1(ROBO2):​c.130+170239C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.1 in 152,124 control chromosomes in the GnomAD database, including 841 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 0.10 (841 hom., cov: 32)
• Consequence: ROBO2 NM_001394212.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.527

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ROBO2	NM_001128929.3	c.109+544054C>T		intron_variant
ROBO2	NM_001378190.1	c.109+544054C>T		intron_variant
ROBO2	NM_001378191.1	c.109+544054C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ROBO2	ENST00000471893.2	c.109+544054C>T		intron_variant		4
ROBO2	ENST00000475334.2	c.130+170239C>T		intron_variant		5		A1
ROBO2	ENST00000487694.7	c.109+544054C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15266 AN: 152004 Hom.: 840 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.131

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0551

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.100 AC: 15281 AN: 152124 Hom.: 841 Cov.: 32 AF XY: 0.0983 AC XY: 7310 AN XY: 74360

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0826

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.00407

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.120

Alfa AF: 0.0988 Hom.: 424

Bravo AF: 0.0989

Asia WGS AF: 0.0720 AC: 251 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13322362; hg19: chr3-76530807;