chr1-160299191-G-A

Variant names:

Variant summary

Our verdict is Benign. The variant received -18 ACMG points: 0P and 18B. BP4_ModerateBP6_Very_StrongBS1BS2

The NM_004371.4(COPA):c.1741C>T(p.Leu581Leu) variant causes a synonymous change. The variant allele was found at a frequency of 0.0311 in 1,614,114 control chromosomes in the GnomAD database, including 875 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.025 ( 51 hom., cov: 32)

Exomes 𝑓: 0.032 ( 824 hom. )

Consequence

COPA
NM_004371.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4O:1

Conservation

PhyloP100: 4.35

Publications

7 publications found

Variant links:

Genes affected

COPA (HGNC:2230): (COPI coat complex subunit alpha) In eukaryotic cells, protein transport between the endoplasmic reticulum and Golgi compartments is mediated in part by non-clathrin-coated vesicular coat proteins (COPs). Seven coat proteins have been identified, and they represent subunits of a complex known as coatomer. The subunits are designated alpha-COP, beta-COP, beta-prime-COP, gamma-COP, delta-COP, epsilon-COP, and zeta-COP. The alpha-COP, encoded by COPA, shares high sequence similarity with RET1P, the alpha subunit of the coatomer complex in yeast. Also, the N-terminal 25 amino acids of alpha-COP encode the bioactive peptide, xenin, which stimulates exocrine pancreatic secretion and may act as a gastrointestinal hormone. Alternative splicing results in multiple splice forms encoding distinct isoforms. [provided by RefSeq, Jul 2008]

COPA Gene-Disease associations (from GenCC):

autoimmune interstitial lung disease-arthritis syndrome
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

COPA links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -18 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BP6

Variant 1-160299191-G-A is Benign according to our data. Variant chr1-160299191-G-A is described in ClinVar as Benign. ClinVar VariationId is 476022.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 = 0.0254 (3871/152248) while in subpopulation NFE AF = 0.0344 (2340/68018). AF 95% confidence interval is 0.0332. There are 51 homozygotes in GnomAd4. There are 1802 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High AC in GnomAd4 at 3871 AD gene.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004371.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	COPA	NM_004371.4	MANE Select	c.1741C>T	p.Leu581Leu	synonymous	Exon 18 of 33	NP_004362.2	P53621-1
	COPA	NM_001098398.2		c.1768C>T	p.Leu590Leu	synonymous	Exon 18 of 33	NP_001091868.1	P53621-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
COPA	ENST00000241704.8	TSL:1 MANE Select	c.1741C>T	p.Leu581Leu	synonymous	Exon 18 of 33	ENSP00000241704.7	P53621-1
COPA	ENST00000368069.7	TSL:1	c.1768C>T	p.Leu590Leu	synonymous	Exon 18 of 33	ENSP00000357048.3	P53621-2
COPA	ENST00000971414.1		c.1762C>T	p.Leu588Leu	synonymous	Exon 18 of 33	ENSP00000641473.1

Frequencies

GnomAD3 genomes

AF:

0.0254

AC:

3870

AN:

152128

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0153

Gnomad AMI

AF:

0.0219

Gnomad AMR

AF:

0.0223

Gnomad ASJ

AF:

0.0311

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0309

Gnomad FIN

AF:

0.0204

Gnomad MID

AF:

0.0316

Gnomad NFE

AF:

0.0344

Gnomad OTH

AF:

0.0249

GnomAD2 exomes

AF:

0.0251

AC:

6324

AN:

251458

AF XY:

0.0268

show subpopulations

Gnomad AFR exome

AF:

0.0137

Gnomad AMR exome

AF:

0.0126

Gnomad ASJ exome

AF:

0.0306

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0179

Gnomad NFE exome

AF:

0.0336

Gnomad OTH exome

AF:

0.0259

GnomAD4 exome

AF:

0.0317

AC:

46356

AN:

1461866

Hom.:

824

Cov.:

AF XY:

0.0320

AC XY:

23269

AN XY:

727238

show subpopulations

African (AFR)

AF:

0.0136

AC:

455

AN:

33480

American (AMR)

AF:

0.0143

AC:

639

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.0282

AC:

738

AN:

26136

East Asian (EAS)

AF:

0.000101

AC:

AN:

39700

South Asian (SAS)

AF:

0.0317

AC:

2737

AN:

86258

European-Finnish (FIN)

AF:

0.0193

AC:

1031

AN:

53420

Middle Eastern (MID)

AF:

0.0321

AC:

185

AN:

5768

European-Non Finnish (NFE)

AF:

0.0349

AC:

38843

AN:

1111986

Other (OTH)

AF:

0.0285

AC:

1724

AN:

60394

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.480

Heterozygous variant carriers

2405

4810

7216

9621

12026

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1460

2920

4380

5840

7300

<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:

0.0254

AC:

3871

AN:

152248

Hom.:

Cov.:

AF XY:

0.0242

AC XY:

1802

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0152

AC:

632

AN:

41550

American (AMR)

AF:

0.0223

AC:

341

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0311

AC:

108

AN:

3472

East Asian (EAS)

AF:

0.000193

AC:

AN:

5186

South Asian (SAS)

AF:

0.0311

AC:

150

AN:

4818

European-Finnish (FIN)

AF:

0.0204

AC:

216

AN:

10594

Middle Eastern (MID)

AF:

0.0374

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0344

AC:

2340

AN:

68018

Other (OTH)

AF:

0.0246

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

197

394

592

789

986

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

192

240

<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:

0.0302

Hom.:

Bravo

AF:

0.0249

Asia WGS

AF:

0.0160

AC:

AN:

3478

EpiCase

AF:

0.0364

EpiControl

AF:

0.0350

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (2)

Autoimmune interstitial lung disease-arthritis syndrome (1)

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

4.4

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.8

Mutation Taster

=97/3

polymorphism (auto)

(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