12-132769223-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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	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	c.*3882G>A		3_prime_UTR_variant	Exon 24 of 24	1	NM_001389683.1	ENSP00000410378.2

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

Gnomad4 AFR exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.0833

Gnomad4 OTH exome AF: 0.250

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

Gnomad4 AFR AF: 0.0610

Gnomad4 AMR AF: 0.0589

Gnomad4 ASJ AF: 0.0740

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.0917

Alfa AF: 0.131 Hom.: 1319

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
DANN	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

Other links and lift over

dbSNP: rs12282; hg19: chr12-133345809;