Genetic Variant GOLGA3:c.*3882G>A (chr12-132769223-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001389683.1(GOLGA3):c.*3882G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 151,746 control chromosomes in the GnomAD database, including 1,024 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 0.11 ( 1024 hom., cov: 33)

Exomes 𝑓: 0.13 ( 0 hom. )

Consequence

GOLGA3
NM_001389683.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.312

Publications

20 publications found

Variant links:

Genes affected

GOLGA3 (HGNC:4426): (golgin A3) The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked cisternae (flattened membrane sacs). Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. This gene encodes a member of the golgin family of proteins which are localized to the Golgi. Its encoded protein has been postulated to play a role in nuclear transport and Golgi apparatus localization. Several alternatively spliced transcript variants that encode different protein isoforms have been described for this gene. [provided by RefSeq, Feb 2010]

GOLGA3 links:

ENSG00000294498 (HGNC:):

ENSG00000294498 links:

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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=-0.9).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GOLGA3	NM_001389683.1 link	c.*3882G>A		3_prime_UTR_variant	Exon 24 of 24	ENST00000450791.8	NP_001376612.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GOLGA3	ENST00000450791.8 link	c.*3882G>A		3_prime_UTR_variant	Exon 24 of 24	1	NM_001389683.1	ENSP00000410378.2		Q08378-1

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16183

AN:

151600

Hom.:

1020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0606

Gnomad AMI

AF:

0.145

Gnomad AMR

AF:

0.0591

Gnomad ASJ

AF:

0.0740

Gnomad EAS

AF:

0.115

Gnomad SAS

AF:

0.162

Gnomad FIN

AF:

0.187

Gnomad MID

AF:

0.0955

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.0931

GnomAD4 exome

AF:

0.133

AC:

AN:

Hom.:

Cov.:

AF XY:

0.136

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0833

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.563

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.107

AC:

16205

AN:

151716

Hom.:

1024

Cov.:

AF XY:

0.108

AC XY:

8040

AN XY:

74196

show subpopulations

African (AFR)

AF:

0.0610

AC:

2533

AN:

41556

American (AMR)

AF:

0.0589

AC:

897

AN:

15230

Ashkenazi Jewish (ASJ)

AF:

0.0740

AC:

255

AN:

3446

East Asian (EAS)

AF:

0.116

AC:

584

AN:

5054

South Asian (SAS)

AF:

0.162

AC:

780

AN:

4806

European-Finnish (FIN)

AF:

0.187

AC:

1986

AN:

10598

Middle Eastern (MID)

AF:

0.0959

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.130

AC:

8818

AN:

67728

Other (OTH)

AF:

0.0917

AC:

193

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

761

1523

2284

3046

3807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

178

356

534

712

890

<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:

0.130

Hom.:

4507

Bravo

AF:

0.0924

Asia WGS

AF:

0.142

AC:

490

AN:

3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.9

(source)

DANN

Benign

0.57

PhyloP100

-0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

Mutation Taster

=100/0

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over