chr3-77061349-C-G

Position:

• chr3-77061349-C-G

Variant summary

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

The NM_001395656.1(ROBO2):​c.61+20503C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,034 control chromosomes in the GnomAD database, including 41,948 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 0.73 (41948 hom., cov: 32)
• Consequence: ROBO2 NM_001395656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ROBO2	NM_001395656.1	c.61+20503C>G		intron_variant		ENST00000696593.1	NP_001382585.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ROBO2	ENST00000696593.1	c.61+20503C>G		intron_variant			NM_001395656.1	ENSP00000512738	A2

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111328 AN: 151916 Hom.: 41942 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.913

Gnomad AMR AF: 0.721

Gnomad ASJ AF: 0.862

Gnomad EAS AF: 0.660

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.770

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.733 AC: 111383 AN: 152034 Hom.: 41948 Cov.: 32 AF XY: 0.731 AC XY: 54335 AN XY: 74300

Gnomad4 AFR AF: 0.556

Gnomad4 AMR AF: 0.721

Gnomad4 ASJ AF: 0.862

Gnomad4 EAS AF: 0.659

Gnomad4 SAS AF: 0.767

Gnomad4 FIN AF: 0.770

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.746

Alfa AF: 0.769 Hom.: 5689

Bravo AF: 0.727

Asia WGS AF: 0.732 AC: 2546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.12
DANN	Benign	0.32

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: rs4476545; hg19: chr3-77110500;