rs12823
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019055.6(ROBO4):c.*176A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 724,856 control chromosomes in the GnomAD database, including 38,781 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 0.29 ( 7151 hom., cov: 32)
Exomes 𝑓: 0.31 ( 31630 hom. )
Consequence
ROBO4
NM_019055.6 3_prime_UTR
NM_019055.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0360
Genes affected
ROBO4 (HGNC:17985): (roundabout guidance receptor 4) Predicted to enable cell-cell adhesion mediator activity. Involved in angiogenesis and establishment of endothelial barrier. Located in extracellular exosome. Implicated in aortic valve disease 3. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.84).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROBO4 | NM_019055.6 | c.*176A>T | 3_prime_UTR_variant | 18/18 | ENST00000306534.8 | ||
ROBO4 | NM_001301088.2 | c.*176A>T | 3_prime_UTR_variant | 18/18 | |||
ROBO4 | XM_006718861.3 | c.*176A>T | 3_prime_UTR_variant | 18/18 | |||
ROBO4 | XM_011542875.2 | c.*176A>T | 3_prime_UTR_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROBO4 | ENST00000306534.8 | c.*176A>T | 3_prime_UTR_variant | 18/18 | 1 | NM_019055.6 | P1 | ||
ROBO4 | ENST00000534407.5 | n.3407A>T | non_coding_transcript_exon_variant | 5/5 | 1 | ||||
ENST00000524453.1 | n.673+352T>A | intron_variant, non_coding_transcript_variant | 3 | ||||||
ROBO4 | ENST00000533054.5 | c.*176A>T | 3_prime_UTR_variant | 18/18 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.292 AC: 44446AN: 152022Hom.: 7157 Cov.: 32
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GnomAD4 exome AF: 0.311 AC: 178352AN: 572716Hom.: 31630 Cov.: 7 AF XY: 0.304 AC XY: 91767AN XY: 302136
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GnomAD4 genome ? AF: 0.292 AC: 44438AN: 152140Hom.: 7151 Cov.: 32 AF XY: 0.285 AC XY: 21185AN XY: 74388
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at