dbSNP rs75002266: ORC4:p.Ala286Val (chr2-147939241-G-A) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_002552.5(ORC4):c.857C>T(p.Ala286Val) variant causes a missense change. The variant allele was found at a frequency of 0.00437 in 1,606,638 control chromosomes in the GnomAD database, including 23 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0030 ( 0 hom., cov: 32)

Exomes 𝑓: 0.0045 ( 23 hom. )

Consequence

ORC4
NM_002552.5 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 6.49

Publications

10 publications found

Variant links:

Genes affected

ORC4 (HGNC:8490): (origin recognition complex subunit 4) 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. This gene encodes a subunit of the ORC complex. Several alternatively spliced transcript variants, some of which encode the same protein, have been reported for this gene. [provided by RefSeq, Oct 2010]

ORC4 Gene-Disease associations (from GenCC):

Meier-Gorlin syndrome 2
Inheritance: AR Classification: DEFINITIVE, STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen, G2P
Meier-Gorlin syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

ORC4 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.013050824).

BP6

Variant 2-147939241-G-A is Benign according to our data. Variant chr2-147939241-G-A is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 436118.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.00302 (459/152234) while in subpopulation NFE AF = 0.005 (340/68012). AF 95% confidence interval is 0.00456. There are 0 homozygotes in GnomAd4. There are 189 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAdExome4 at 23 AR,AD gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002552.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ORC4	NM_181741.4	MANE Select	c.857C>T	p.Ala286Val	missense	Exon 11 of 14	NP_859525.1
ORC4	NM_001190879.3		c.857C>T	p.Ala286Val	missense	Exon 12 of 15	NP_001177808.1
ORC4	NM_001374270.1		c.857C>T	p.Ala286Val	missense	Exon 13 of 16	NP_001361199.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein
ORC4	ENST00000392857.10	TSL:1 MANE Select	c.857C>T	p.Ala286Val	missense	Exon 11 of 14	ENSP00000376597.5
ORC4	ENST00000877934.1		c.857C>T	p.Ala286Val	missense	Exon 11 of 15	ENSP00000547993.1
ORC4	ENST00000264169.6	TSL:5	c.857C>T	p.Ala286Val	missense	Exon 11 of 14	ENSP00000264169.2

Frequencies

GnomAD3 genomes

AF:

0.00302

AC:

459

AN:

152116

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000748

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.00778

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.000283

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00500

Gnomad OTH

AF:

0.00622

GnomAD2 exomes

AF:

0.00320

AC:

804

AN:

250942

AF XY:

0.00345

show subpopulations

Gnomad AFR exome

AF:

0.000492

Gnomad AMR exome

AF:

0.00226

Gnomad ASJ exome

AF:

0.00895

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.000463

Gnomad NFE exome

AF:

0.00509

Gnomad OTH exome

AF:

0.00360

GnomAD4 exome

AF:

0.00452

AC:

6568

AN:

1454404

Hom.:

Cov.:

AF XY:

0.00452

AC XY:

3269

AN XY:

724008

show subpopulations

African (AFR)

AF:

0.000780

AC:

AN:

33318

American (AMR)

AF:

0.00280

AC:

125

AN:

44682

Ashkenazi Jewish (ASJ)

AF:

0.00864

AC:

225

AN:

26056

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39618

South Asian (SAS)

AF:

0.000441

AC:

AN:

86106

European-Finnish (FIN)

AF:

0.000431

AC:

AN:

53350

Middle Eastern (MID)

AF:

0.0160

AC:

AN:

5754

European-Non Finnish (NFE)

AF:

0.00521

AC:

5757

AN:

1105438

Other (OTH)

AF:

0.00468

AC:

281

AN:

60082

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

287

574

860

1147

1434

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

220

440

660

880

1100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00302

AC:

459

AN:

152234

Hom.:

Cov.:

AF XY:

0.00254

AC XY:

189

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.000746

AC:

AN:

41544

American (AMR)

AF:

0.00249

AC:

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.00778

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5182

South Asian (SAS)

AF:

0.000414

AC:

AN:

4830

European-Finnish (FIN)

AF:

0.000283

AC:

AN:

10608

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00500

AC:

340

AN:

68012

Other (OTH)

AF:

0.00616

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

119

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00456

Hom.:

Bravo

AF:

0.00346

TwinsUK

AF:

0.00782

AC:

ALSPAC

AF:

0.00675

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00593

AC:

ExAC

AF:

0.00315

AC:

382

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00605

EpiControl

AF:

0.00723

ClinVar

ClinVar submissions as Germline

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (3)

not specified (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.17

BayesDel_noAF

Uncertain

-0.020

CADD

Benign

(source)

DANN

Benign

0.72

DEOGEN2

Benign

0.018

Eigen

Benign

0.16

Eigen_PC

Uncertain

0.28

FATHMM_MKL

Uncertain

0.80

LIST_S2

Uncertain

0.86

M_CAP

Benign

0.024

MetaRNN

Benign

0.013

MetaSVM

Benign

-0.48

MutationAssessor

Uncertain

2.1

PhyloP100

6.5

PrimateAI

Benign

0.31

PROVEAN

Benign

-0.68

REVEL

Uncertain

0.42

Sift

Benign

1.0

Sift4G

Benign

0.66

Polyphen

0.22

Vest4

0.69

MVP

0.87

MPC

0.11

ClinPred

0.025

GERP RS

5.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Varity_R

0.25

gMVP

0.41

Mutation Taster

=94/6

polymorphism

(source)

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over