NM_001389683.1:c.*3882G>A

Variant names:

• chr12-132769223-C-T
• rs12282
• NM_001389683.1:c.*3882G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312
• Publications: 20 publications found

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]

ENSG00000294498 (HGNC:):

ACMG classification

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001389683.1. 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
	GOLGA3	NM_001389683.1	MANE Select	c.*3882G>A		3_prime_UTR	Exon 24 of 24	NP_001376612.1	Q08378-1
	GOLGA3	NM_001389684.1		c.*3882G>A		3_prime_UTR	Exon 24 of 24	NP_001376613.1	Q08378-1
	GOLGA3	NM_001389685.1		c.*3882G>A		3_prime_UTR	Exon 26 of 26	NP_001376614.1	Q08378-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GOLGA3	ENST00000450791.8	TSL:1 MANE Select	c.*3882G>A		3_prime_UTR	Exon 24 of 24	ENSP00000410378.2	Q08378-1
	GOLGA3	ENST00000204726.9	TSL:5	c.*3882G>A		3_prime_UTR	Exon 24 of 24	ENSP00000204726.3	Q08378-1
	GOLGA3	ENST00000688114.1		c.*3882G>A		3_prime_UTR	Exon 24 of 24	ENSP00000510765.1	A0A8I5KWY9

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16183 AN: 151600 Hom.: 1020 Cov.: 33

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: 4 AN: 30 Hom.: 0 Cov.: 0 AF XY: 0.136 AC XY: 3 AN XY: 22

African (AFR) AF: 0.500 AC: 1 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.125 AC: 1 AN: 8

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.0833 AC: 1 AN: 12

Other (OTH) AF: 0.250 AC: 1 AN: 4

GnomAD4 genome AF: 0.107 AC: 16205 AN: 151716 Hom.: 1024 Cov.: 33 AF XY: 0.108 AC XY: 8040 AN XY: 74196

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: 28 AN: 292

European-Non Finnish (NFE) AF: 0.130 AC: 8818 AN: 67728

Other (OTH) AF: 0.0917 AC: 193 AN: 2104

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
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)

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

Other links and lift over

dbSNP: rs12282; hg19: chr12-133345809;