6-87603451-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012381.4(ORC3):āc.245C>Gā(p.Ser82Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000522 in 1,531,484 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 (ā ).
Frequency
Consequence
NM_012381.4 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 |
---|---|---|---|---|---|---|---|
ORC3 | NM_012381.4 | c.245C>G | p.Ser82Cys | missense_variant | 4/20 | ENST00000392844.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ORC3 | ENST00000392844.8 | c.245C>G | p.Ser82Cys | missense_variant | 4/20 | 1 | NM_012381.4 | A1 | |
ORC3 | ENST00000257789.4 | c.245C>G | p.Ser82Cys | missense_variant | 4/20 | 1 | P4 | ||
ORC3 | ENST00000546266.5 | c.-185C>G | 5_prime_UTR_variant | 3/19 | 2 | ||||
ORC3 | ENST00000681069.1 | n.278C>G | non_coding_transcript_exon_variant | 4/15 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250378Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135354
GnomAD4 exome AF: 0.00000290 AC: 4AN: 1379332Hom.: 0 Cov.: 26 AF XY: 0.00000293 AC XY: 2AN XY: 682638
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152152Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 09, 2021 | The c.245C>G (p.S82C) alteration is located in exon 4 (coding exon 4) of the ORC3 gene. This alteration results from a C to G substitution at nucleotide position 245, causing the serine (S) at amino acid position 82 to be replaced by a cysteine (C). 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