rs1666130

chr3-77549792-C-T

Variant summary

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

The NM_001395656.1(ROBO2):c.1072-1026C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.56 in 151,746 control chromosomes in the GnomAD database, including 23,866 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 0.56 (23866 hom., cov: 32)
• Consequence: ROBO2 NM_001395656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.48

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=-0.47).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ROBO2	NM_001395656.1	c.1072-1026C>T		intron_variant		ENST00000696593.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ROBO2	ENST00000696593.1	c.1072-1026C>T		intron_variant			NM_001395656.1	A2

Frequencies

GnomAD3 genomes AF: 0.560 AC: 84924 AN: 151628 Hom.: 23856 Cov.: 32

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.496

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.594

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

GnomAD4 genome AF: 0.560 AC: 84969 AN: 151746 Hom.: 23866 Cov.: 32 AF XY: 0.561 AC XY: 41591 AN XY: 74132

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.524

Gnomad4 SAS AF: 0.564

Gnomad4 FIN AF: 0.496

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.591

Alfa AF: 0.558 Hom.: 36671

Bravo AF: 0.569

Asia WGS AF: 0.543 AC: 1887 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
Cadd	Benign	19
Dann	Benign	0.50

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

Other links and lift over

dbSNP: rs1666130; hg19: chr3-77598943; COSMIC: COSV59916642;