rs10167387

Variant names:

• chr2-200943895-T-C
• rs10167387
• NM_006190.5:c.329-1118A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006190.5(ORC2):​c.329-1118A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 151,752 control chromosomes in the GnomAD database, including 10,808 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.32 (10808 hom., cov: 30)
• Consequence: ORC2 NM_006190.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.236
• Publications: 18 publications found

Genes affected

ORC2 (HGNC:8488): (origin recognition complex subunit 2) The origin recognition complex (ORC) is a highly conserved six subunits 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. This protein forms a core complex with ORC3, -4, and -5. It also interacts with CDC45 and MCM10, which are proteins known to be important for the initiation of DNA replication. This protein has been demonstrated to specifically associate with the origin of replication of Epstein-Barr virus in human cells, and is thought to be required for DNA replication from viral origin of replication. Alternatively spliced transcript variants have been found, one of which is a nonsense-mediated mRNA decay candidate. [provided by RefSeq, Oct 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006190.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ORC2	NM_006190.5	MANE Select	c.329-1118A>G		intron	N/A	NP_006181.1
	ORC2	NR_033915.2		n.559-1118A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ORC2	ENST00000234296.7	TSL:1 MANE Select	c.329-1118A>G		intron	N/A	ENSP00000234296.2
	ORC2	ENST00000938732.1		c.329-748A>G		intron	N/A	ENSP00000608791.1
	ORC2	ENST00000879137.1		c.374-1118A>G		intron	N/A	ENSP00000549196.1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49166 AN: 151634 Hom.: 10779 Cov.: 30

Gnomad AFR AF: 0.624

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.211

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0127

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.204

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.293

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.325 AC: 49258 AN: 151752 Hom.: 10808 Cov.: 30 AF XY: 0.319 AC XY: 23661 AN XY: 74204

African (AFR) AF: 0.625 AC: 25784 AN: 41282

American (AMR) AF: 0.211 AC: 3209 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1166 AN: 3468

East Asian (EAS) AF: 0.0128 AC: 66 AN: 5168

South Asian (SAS) AF: 0.154 AC: 743 AN: 4814

European-Finnish (FIN) AF: 0.204 AC: 2147 AN: 10544

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15271 AN: 67920

Other (OTH) AF: 0.298 AC: 630 AN: 2112

Alfa AF: 0.262 Hom.: 12144

Bravo AF: 0.337

Asia WGS AF: 0.145 AC: 508 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.3
DANN	Benign	0.82
PhyloP100		0.24
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10167387; hg19: chr2-201808618;