11-124895272-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_019055.6(ROBO4):c.1037-79G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 1,247,086 control chromosomes in the GnomAD database, including 16,735 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 0.16 ( 1999 hom., cov: 32)
Exomes 𝑓: 0.16 ( 14736 hom. )
Consequence
ROBO4
NM_019055.6 intron
NM_019055.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0850
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=-0.8).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ROBO4 | NM_019055.6 | c.1037-79G>A | intron_variant | Intron 6 of 17 | ENST00000306534.8 | NP_061928.4 | ||
ROBO4 | NM_001301088.2 | c.602-79G>A | intron_variant | Intron 6 of 17 | NP_001288017.1 | |||
ROBO4 | XM_006718861.3 | c.1037-79G>A | intron_variant | Intron 6 of 17 | XP_006718924.1 | |||
LOC107984406 | XR_001748429.3 | n.334+3140C>T | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.159 AC: 24072AN: 151854Hom.: 1999 Cov.: 32
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GnomAD4 exome AF: 0.160 AC: 175575AN: 1095114Hom.: 14736 Cov.: 14 AF XY: 0.162 AC XY: 90152AN XY: 556906
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GnomAD4 genome AF: 0.158 AC: 24084AN: 151972Hom.: 1999 Cov.: 32 AF XY: 0.165 AC XY: 12262AN XY: 74300
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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