3-75937544-G-A
Position:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2
The NM_001378191.1(ROBO2):c.51G>A(p.Pro17=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000491 in 1,425,304 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000049 ( 0 hom. )
Consequence
ROBO2
NM_001378191.1 synonymous
NM_001378191.1 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.34
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 -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 3-75937544-G-A is Benign according to our data. Variant chr3-75937544-G-A is described in ClinVar as [Benign]. Clinvar id is 3059993.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-2.34 with no splicing effect.
BS2
High AC in GnomAdExome4 at 7 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| ROBO2 | NM_001378191.1 | c.51G>A | p.Pro17= | synonymous_variant | 2/30 | NP_001365120.1 | ||
| ROBO2 | NM_001378190.1 | c.51G>A | p.Pro17= | synonymous_variant | 2/29 | NP_001365119.1 | ||
| ROBO2 | NM_001378195.1 | c.51G>A | p.Pro17= | synonymous_variant | 2/29 | NP_001365124.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| ROBO2 | ENST00000696630.1 | c.51G>A | p.Pro17= | synonymous_variant | 2/30 | ENSP00000512767 | ||||
| ROBO2 | ENST00000696629.1 | c.51G>A | p.Pro17= | synonymous_variant | 2/29 | ENSP00000512766 | ||||
| ROBO2 | ENST00000471893.2 | c.51G>A | p.Pro17= | synonymous_variant | 2/29 | 4 | ENSP00000418190 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000491 AC: 7AN: 1425304Hom.: 0 Cov.: 30 AF XY: 0.00000706 AC XY: 5AN XY: 707940
GnomAD4 exome
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30
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707940
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GnomAD4 genome
GnomAD4 genome
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32
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
ROBO2-related disorder Benign:1
| Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 18, 2020 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational 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