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

Genomes: 𝑓 0.000026 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000045 ( 0 hom. )

Consequence

ORC5
NM_002553.4 missense

Scores

19

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.621
Variant links:
Genes affected
ORC5 (HGNC:8491): (origin recognition complex subunit 5) The origin recognition complex (ORC) is a highly conserved six subunit protein complex essential for the initiation of the DNA replication in eukaryotic cells. Studies in yeast demonstrated that ORC binds specifically to origins of replication and serves as a platform for the assembly of additional initiation factors such as Cdc6 and Mcm proteins. The protein encoded by this gene is a subunit of the ORC complex. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Oct 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.02743715).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ORC5NM_002553.4 linkuse as main transcriptc.863C>T p.Pro288Leu missense_variant 9/14 ENST00000297431.9 NP_002544.1
ORC5NM_181747.4 linkuse as main transcriptc.863C>T p.Pro288Leu missense_variant 9/9 NP_859531.1
ORC5XM_047420431.1 linkuse as main transcriptc.*9C>T 3_prime_UTR_variant 7/8 XP_047276387.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ORC5ENST00000297431.9 linkuse as main transcriptc.863C>T p.Pro288Leu missense_variant 9/141 NM_002553.4 ENSP00000297431 P1O43913-1
ORC5ENST00000447452.6 linkuse as main transcriptc.863C>T p.Pro288Leu missense_variant 9/91 ENSP00000395747 O43913-2
ORC5ENST00000422497.5 linkuse as main transcriptc.*796C>T 3_prime_UTR_variant, NMD_transcript_variant 10/152 ENSP00000393208

Frequencies

GnomAD3 genomes
AF:
0.0000264
AC:
4
AN:
151754
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000242
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000294
Gnomad OTH
AF:
0.000480
GnomAD3 exomes
AF:
0.0000376
AC:
9
AN:
239534
Hom.:
0
AF XY:
0.0000308
AC XY:
4
AN XY:
129870
show subpopulations
Gnomad AFR exome
AF:
0.0000624
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000113
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000546
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000450
AC:
65
AN:
1444526
Hom.:
0
Cov.:
29
AF XY:
0.0000487
AC XY:
35
AN XY:
718596
show subpopulations
Gnomad4 AFR exome
AF:
0.0000909
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000102
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000525
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000264
AC:
4
AN:
151754
Hom.:
0
Cov.:
32
AF XY:
0.0000270
AC XY:
2
AN XY:
74128
show subpopulations
Gnomad4 AFR
AF:
0.0000242
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000294
Gnomad4 OTH
AF:
0.000480
Alfa
AF:
0.0000581
Hom.:
0
Bravo
AF:
0.0000189
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000412
AC:
5

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMay 28, 2023The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.060
BayesDel_addAF
Benign
-0.48
T
BayesDel_noAF
Benign
-0.70
CADD
Benign
15
DANN
Benign
0.41
DEOGEN2
Benign
0.021
T;.
Eigen
Benign
-0.85
Eigen_PC
Benign
-0.80
FATHMM_MKL
Benign
0.47
N
LIST_S2
Benign
0.74
T;T
M_CAP
Benign
0.0086
T
MetaRNN
Benign
0.027
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.55
N;N
MutationTaster
Benign
1.0
N;N;N
PrimateAI
Benign
0.30
T
PROVEAN
Benign
-0.17
N;N
REVEL
Benign
0.052
Sift
Benign
0.39
T;T
Sift4G
Benign
0.39
T;T
Polyphen
0.0
B;B
Vest4
0.17
MVP
0.26
MPC
0.077
ClinPred
0.0061
T
GERP RS
-1.1
Varity_R
0.048
gMVP
0.39

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.12
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs368195311; hg19: chr7-103808935; COSMIC: COSV52397523; COSMIC: COSV52397523; API