7-104168487-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002553.4(ORC5):c.863C>T(p.Pro288Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000432 in 1,596,280 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002553.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ORC5 | NM_002553.4 | c.863C>T | p.Pro288Leu | missense_variant | 9/14 | ENST00000297431.9 | NP_002544.1 | |
ORC5 | NM_181747.4 | c.863C>T | p.Pro288Leu | missense_variant | 9/9 | NP_859531.1 | ||
ORC5 | XM_047420431.1 | c.*9C>T | 3_prime_UTR_variant | 7/8 | XP_047276387.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ORC5 | ENST00000297431.9 | c.863C>T | p.Pro288Leu | missense_variant | 9/14 | 1 | NM_002553.4 | ENSP00000297431 | P1 | |
ORC5 | ENST00000447452.6 | c.863C>T | p.Pro288Leu | missense_variant | 9/9 | 1 | ENSP00000395747 | |||
ORC5 | ENST00000422497.5 | c.*796C>T | 3_prime_UTR_variant, NMD_transcript_variant | 10/15 | 2 | ENSP00000393208 |
Frequencies
GnomAD3 genomes AF: 0.0000264 AC: 4AN: 151754Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000376 AC: 9AN: 239534Hom.: 0 AF XY: 0.0000308 AC XY: 4AN XY: 129870
GnomAD4 exome AF: 0.0000450 AC: 65AN: 1444526Hom.: 0 Cov.: 29 AF XY: 0.0000487 AC XY: 35AN XY: 718596
GnomAD4 genome AF: 0.0000264 AC: 4AN: 151754Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74128
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 28, 2023 | The c.863C>T (p.P288L) alteration is located in exon 9 (coding exon 9) of the ORC5 gene. This alteration results from a C to T substitution at nucleotide position 863, causing the proline (P) at amino acid position 288 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