rs3907672
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001394212.1(ROBO2):c.130+99278T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.187 in 152,136 control chromosomes in the GnomAD database, including 3,112 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 0.19 ( 3112 hom., cov: 32)
Consequence
ROBO2
NM_001394212.1 intron
NM_001394212.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.151
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROBO2 | NM_001128929.3 | c.109+473093T>C | intron_variant | ||||
ROBO2 | NM_001378190.1 | c.109+473093T>C | intron_variant | ||||
ROBO2 | NM_001378191.1 | c.109+473093T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROBO2 | ENST00000471893.2 | c.109+473093T>C | intron_variant | 4 | |||||
ROBO2 | ENST00000475334.2 | c.130+99278T>C | intron_variant | 5 | A1 | ||||
ROBO2 | ENST00000487694.7 | c.109+473093T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.187 AC: 28364AN: 152018Hom.: 3116 Cov.: 32
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?
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.187 AC: 28375AN: 152136Hom.: 3112 Cov.: 32 AF XY: 0.182 AC XY: 13526AN XY: 74382
GnomAD4 genome
?
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32
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13526
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74382
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248
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3470
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at