chr11-124885137-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019055.6(ROBO4):c.2905A>C(p.Thr969Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,766 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T969T) has been classified as Benign.
Frequency
Consequence
NM_019055.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROBO4 | NM_019055.6 | c.2905A>C | p.Thr969Pro | missense_variant | 17/18 | ENST00000306534.8 | |
ROBO4 | NM_001301088.2 | c.2470A>C | p.Thr824Pro | missense_variant | 17/18 | ||
ROBO4 | XM_006718861.3 | c.2791A>C | p.Thr931Pro | missense_variant | 17/18 | ||
ROBO4 | XM_011542875.2 | c.1579A>C | p.Thr527Pro | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROBO4 | ENST00000306534.8 | c.2905A>C | p.Thr969Pro | missense_variant | 17/18 | 1 | NM_019055.6 | P1 | |
ROBO4 | ENST00000534407.5 | n.3112A>C | non_coding_transcript_exon_variant | 4/5 | 1 | ||||
ENST00000524453.1 | n.673+774T>G | intron_variant, non_coding_transcript_variant | 3 | ||||||
ROBO4 | ENST00000533054.5 | c.2470A>C | p.Thr824Pro | missense_variant | 17/18 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461766Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727198
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 14, 2023 | The c.2905A>C (p.T969P) alteration is located in exon 17 (coding exon 17) of the ROBO4 gene. This alteration results from a A to C substitution at nucleotide position 2905, causing the threonine (T) at amino acid position 969 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.