Variant rs11170877 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 8P and 8B. PVS1BA1

The NM_001271736.2(COPZ1):c.1A>G(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 1,611,242 control chromosomes in the GnomAD database, including 15,917 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 0.17 ( 2371 hom., cov: 31)

Exomes 𝑓: 0.13 ( 13546 hom. )

Consequence

COPZ1
NM_001271736.2 start_lost

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.183

Variant links:

Genes affected

COPZ1 (HGNC:2243): (COPI coat complex subunit zeta 1) This gene encodes a subunit of the cytoplasmic coatamer protein complex, which is involved in autophagy and intracellular protein trafficking. The coatomer protein complex is comprised of seven subunits and functions as the coat protein of coat protein complex (COP)I-vesicles. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2012]

COPZ1 links:

ENSG00000258344 (HGNC:):

ENSG00000258344 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PVS1

Start lost variant, no new inframe start found.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
COPZ1	NM_016057.3 link	c.19-42A>G		intron_variant		ENST00000262061.7	NP_057141.1	P61923-1A0A024RB72

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
COPZ1	ENST00000262061.7 link	c.19-42A>G		intron_variant		1	NM_016057.3	ENSP00000262061.2		P61923-1

Frequencies

GnomAD3 genomes

AF:

0.166

AC:

25195

AN:

151922

Hom.:

2357

Cov.:

show subpopulations

Gnomad AFR

AF:

0.233

Gnomad AMI

AF:

0.0515

Gnomad AMR

AF:

0.210

Gnomad ASJ

AF:

0.0706

Gnomad EAS

AF:

0.233

Gnomad SAS

AF:

0.141

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.112

Gnomad OTH

AF:

0.141

GnomAD3 exomes

AF:

0.156

AC:

38821

AN:

248782

Hom.:

3587

AF XY:

0.149

AC XY:

19997

AN XY:

134580

show subpopulations

Gnomad AFR exome

AF:

0.233

Gnomad AMR exome

AF:

0.249

Gnomad ASJ exome

AF:

0.0692

Gnomad EAS exome

AF:

0.227

Gnomad SAS exome

AF:

0.138

Gnomad FIN exome

AF:

0.197

Gnomad NFE exome

AF:

0.112

Gnomad OTH exome

AF:

0.128

GnomAD4 exome

AF:

0.129

AC:

187628

AN:

1459202

Hom.:

13546

Cov.:

AF XY:

0.127

AC XY:

92332

AN XY:

725982

show subpopulations

Gnomad4 AFR exome

AF:

0.233

Gnomad4 AMR exome

AF:

0.242

Gnomad4 ASJ exome

AF:

0.0708

Gnomad4 EAS exome

AF:

0.255

Gnomad4 SAS exome

AF:

0.132

Gnomad4 FIN exome

AF:

0.190

Gnomad4 NFE exome

AF:

0.115

Gnomad4 OTH exome

AF:

0.131

GnomAD4 genome

AF:

0.166

AC:

25247

AN:

152040

Hom.:

2371

Cov.:

AF XY:

0.172

AC XY:

12800

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.233

Gnomad4 AMR

AF:

0.210

Gnomad4 ASJ

AF:

0.0706

Gnomad4 EAS

AF:

0.234

Gnomad4 SAS

AF:

0.140

Gnomad4 FIN

AF:

0.213

Gnomad4 NFE

AF:

0.112

Gnomad4 OTH

AF:

0.145

Alfa

AF:

0.117

Hom.:

2038

Bravo

AF:

0.166

TwinsUK

AF:

0.121

AC:

447

ALSPAC

AF:

0.117

AC:

451

ESP6500AA

AF:

0.231

AC:

1016

ESP6500EA

AF:

0.111

AC:

958

ExAC

AF:

0.152

AC:

18515

Asia WGS

AF:

0.236

AC:

819

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.54

BayesDel_noAF

Benign

-0.41

CADD

Benign

DANN

Benign

0.82

DEOGEN2

Benign

0.0074

.;T

Eigen

Benign

-0.92

Eigen_PC

Benign

-0.96

FATHMM_MKL

Benign

0.00038

LIST_S2

Uncertain

0.90

D;D

MetaRNN

Benign

0.0044

T;T

MetaSVM

Benign

-1.1

PROVEAN

Benign

-0.22

N;N

REVEL

Benign

0.13

Sift

Pathogenic

0.0

D;D

Sift4G

Benign

0.17

T;T

Vest4

0.057

ClinPred

0.017

GERP RS

2.5

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

gMVP

0.44

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over