chr2-200914227-A-G

Variant names:

• chr2-200914227-A-G
• rs10172647
• NM_006190.5:c.1467-235T>C

Variant summary

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

The NM_006190.5(ORC2):​c.1467-235T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 147,220 control chromosomes in the GnomAD database, including 9,656 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 (9656 hom., cov: 26)
• Consequence: ORC2 NM_006190.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 9 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=-1.06).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.589 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ORC2	NM_006190.5	c.1467-235T>C		intron_variant	Intron 15 of 17	ENST00000234296.7	NP_006181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ORC2	ENST00000234296.7	c.1467-235T>C		intron_variant	Intron 15 of 17	1	NM_006190.5	ENSP00000234296.2
ORC2	ENST00000464147.1	n.554-235T>C		intron_variant	Intron 4 of 5	5

Frequencies

GnomAD3 genomes AF: 0.317 AC: 46654 AN: 147124 Hom.: 9631 Cov.: 26

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.0129

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.317 AC: 46735 AN: 147220 Hom.: 9656 Cov.: 26 AF XY: 0.314 AC XY: 22394 AN XY: 71274

African (AFR) AF: 0.595 AC: 23752 AN: 39896

American (AMR) AF: 0.212 AC: 3053 AN: 14372

Ashkenazi Jewish (ASJ) AF: 0.336 AC: 1160 AN: 3454

East Asian (EAS) AF: 0.0130 AC: 64 AN: 4938

South Asian (SAS) AF: 0.154 AC: 722 AN: 4686

European-Finnish (FIN) AF: 0.219 AC: 2054 AN: 9396

Middle Eastern (MID) AF: 0.224 AC: 64 AN: 286

European-Non Finnish (NFE) AF: 0.225 AC: 15112 AN: 67268

Other (OTH) AF: 0.289 AC: 584 AN: 2024

Alfa AF: 0.287 Hom.: 986

Bravo AF: 0.327

Asia WGS AF: 0.137 AC: 479 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.21
DANN	Benign	0.11
PhyloP100		-2.8
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: rs10172647; hg19: chr2-201778950;