chr11-124886510-G-A
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_019055.6(ROBO4):c.2748C>T(p.Ser916=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 1,613,978 control chromosomes in the GnomAD database, including 23,521 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.22 ( 4941 hom., cov: 33)
Exomes 𝑓: 0.15 ( 18580 hom. )
Consequence
ROBO4
NM_019055.6 synonymous
NM_019055.6 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.801
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 11-124886510-G-A is Benign according to our data. Variant chr11-124886510-G-A is described in ClinVar as [Benign]. Clinvar id is 2691020.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.801 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROBO4 | NM_019055.6 | c.2748C>T | p.Ser916= | synonymous_variant | 16/18 | ENST00000306534.8 | |
ROBO4 | NM_001301088.2 | c.2313C>T | p.Ser771= | synonymous_variant | 16/18 | ||
ROBO4 | XM_006718861.3 | c.2634C>T | p.Ser878= | synonymous_variant | 16/18 | ||
ROBO4 | XM_011542875.2 | c.1422C>T | p.Ser474= | synonymous_variant | 9/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROBO4 | ENST00000306534.8 | c.2748C>T | p.Ser916= | synonymous_variant | 16/18 | 1 | NM_019055.6 | P1 | |
ENST00000524453.1 | n.674-1209G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.223 AC: 33981AN: 152060Hom.: 4926 Cov.: 33
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GnomAD3 exomes AF: 0.164 AC: 41308AN: 251210Hom.: 4206 AF XY: 0.163 AC XY: 22078AN XY: 135816
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GnomAD4 exome AF: 0.151 AC: 221139AN: 1461800Hom.: 18580 Cov.: 33 AF XY: 0.152 AC XY: 110450AN XY: 727204
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GnomAD4 genome ? AF: 0.224 AC: 34027AN: 152178Hom.: 4941 Cov.: 33 AF XY: 0.226 AC XY: 16816AN XY: 74410
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial thoracic aortic aneurysm and aortic dissection Benign:1
Benign, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Nov 18, 2022 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at