11-124885169-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019055.6(ROBO4):c.2873C>T(p.Pro958Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,700 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ROBO4 | NM_019055.6 | c.2873C>T | p.Pro958Leu | missense_variant | 17/18 | ENST00000306534.8 | NP_061928.4 | |
ROBO4 | NM_001301088.2 | c.2438C>T | p.Pro813Leu | missense_variant | 17/18 | NP_001288017.1 | ||
ROBO4 | XM_006718861.3 | c.2759C>T | p.Pro920Leu | missense_variant | 17/18 | XP_006718924.1 | ||
ROBO4 | XM_011542875.2 | c.1547C>T | p.Pro516Leu | missense_variant | 10/11 | XP_011541177.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ROBO4 | ENST00000306534.8 | c.2873C>T | p.Pro958Leu | missense_variant | 17/18 | 1 | NM_019055.6 | ENSP00000304945.3 | ||
ROBO4 | ENST00000534407.5 | n.3080C>T | non_coding_transcript_exon_variant | 4/5 | 1 | |||||
ROBO4 | ENST00000533054.5 | c.2438C>T | p.Pro813Leu | missense_variant | 17/18 | 2 | ENSP00000437129.1 | |||
ENSG00000254568 | ENST00000524453.1 | n.673+806G>A | intron_variant | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461700Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727174
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2024 | The c.2873C>T (p.P958L) alteration is located in exon 17 (coding exon 17) of the ROBO4 gene. This alteration results from a C to T substitution at nucleotide position 2873, causing the proline (P) at amino acid position 958 to be replaced by a leucine (L). 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