dbSNP rs2072575: COPG2:c.2150-7C>T (chr7-130508666-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_012133.6(COPG2):c.2150-7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 753,252 control chromosomes in the GnomAD database, including 101,888 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 0.43 ( 16664 hom., cov: 31)

Exomes 𝑓: 0.53 ( 85224 hom. )

Consequence

COPG2
NM_012133.6 splice_region, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.293

Publications

9 publications found

Variant links:

Genes affected

COPG2 (HGNC:2237): (COPI coat complex subunit gamma 2) Predicted to enable structural molecule activity. Involved in intra-Golgi vesicle-mediated transport. Part of COPI vesicle coat. [provided by Alliance of Genome Resources, Apr 2022]

COPG2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.568 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
COPG2	NM_012133.6 link	c.2150-7C>T		splice_region_variant, intron_variant	Intron 20 of 23	ENST00000425248.5	NP_036265.3	Q9UBF2-1A0A140VK12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
COPG2	ENST00000425248.5 link	c.2150-7C>T		splice_region_variant, intron_variant	Intron 20 of 23	1	NM_012133.6	ENSP00000402346.2		Q9UBF2-1
COPG2	ENST00000617523.1 link	n.1531-7C>T		splice_region_variant, intron_variant	Intron 11 of 14	5

Frequencies

GnomAD3 genomes

AF:

0.425

AC:

64594

AN:

151876

Hom.:

16664

Cov.:

show subpopulations

Gnomad AFR

AF:

0.118

Gnomad AMI

AF:

0.459

Gnomad AMR

AF:

0.515

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.586

Gnomad SAS

AF:

0.492

Gnomad FIN

AF:

0.564

Gnomad MID

AF:

0.396

Gnomad NFE

AF:

0.548

Gnomad OTH

AF:

0.443

GnomAD2 exomes

AF:

0.515

AC:

105474

AN:

204932

AF XY:

0.516

show subpopulations

Gnomad AFR exome

AF:

0.107

Gnomad AMR exome

AF:

0.537

Gnomad ASJ exome

AF:

0.519

Gnomad EAS exome

AF:

0.590

Gnomad FIN exome

AF:

0.564

Gnomad NFE exome

AF:

0.546

Gnomad OTH exome

AF:

0.504

GnomAD4 exome

AF:

0.526

AC:

316096

AN:

601258

Hom.:

85224

Cov.:

AF XY:

0.524

AC XY:

170805

AN XY:

325808

show subpopulations

African (AFR)

AF:

0.115

AC:

2001

AN:

17348

American (AMR)

AF:

0.527

AC:

20472

AN:

38848

Ashkenazi Jewish (ASJ)

AF:

0.512

AC:

10490

AN:

20472

East Asian (EAS)

AF:

0.602

AC:

21162

AN:

35174

South Asian (SAS)

AF:

0.482

AC:

31426

AN:

65236

European-Finnish (FIN)

AF:

0.562

AC:

29049

AN:

51692

Middle Eastern (MID)

AF:

0.354

AC:

1453

AN:

4104

European-Non Finnish (NFE)

AF:

0.547

AC:

184008

AN:

336210

Other (OTH)

AF:

0.498

AC:

16035

AN:

32174

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.493

Heterozygous variant carriers

7710

15420

23129

30839

38549

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

974

1948

2922

3896

4870

<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:

0.425

AC:

64601

AN:

151994

Hom.:

16664

Cov.:

AF XY:

0.429

AC XY:

31887

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.118

AC:

4878

AN:

41512

American (AMR)

AF:

0.515

AC:

7855

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.534

AC:

1852

AN:

3468

East Asian (EAS)

AF:

0.586

AC:

3023

AN:

5162

South Asian (SAS)

AF:

0.493

AC:

2370

AN:

4810

European-Finnish (FIN)

AF:

0.564

AC:

5935

AN:

10532

Middle Eastern (MID)

AF:

0.425

AC:

125

AN:

294

European-Non Finnish (NFE)

AF:

0.548

AC:

37216

AN:

67938

Other (OTH)

AF:

0.441

AC:

929

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1630

3259

4889

6518

8148

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

594

1188

1782

2376

2970

<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:

0.475

Hom.:

8223

Bravo

AF:

0.410

Asia WGS

AF:

0.530

AC:

1842

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

8.5

(source)

DANN

Benign

0.80

PhyloP100

0.29

Splicing

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over