3-37248331-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002078.5(GOLGA4):c.73-3064C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,210 control chromosomes in the GnomAD database, including 56,219 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 0.85 ( 56219 hom., cov: 31)
Consequence
GOLGA4
NM_002078.5 intron
NM_002078.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.84
Publications
5 publications found
Genes affected
GOLGA4 (HGNC:4427): (golgin A4) 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 one of the golgins, a family of proteins localized to the Golgi. This protein has been postulated to play a role in Rab6-regulated membrane-tethering events in the Golgi apparatus. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, Feb 2010]
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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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.854 AC: 129919AN: 152092Hom.: 56174 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
129919
AN:
152092
Hom.:
Cov.:
31
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.854 AC: 130025AN: 152210Hom.: 56219 Cov.: 31 AF XY: 0.847 AC XY: 63011AN XY: 74426 show subpopulations
GnomAD4 genome
AF:
AC:
130025
AN:
152210
Hom.:
Cov.:
31
AF XY:
AC XY:
63011
AN XY:
74426
show subpopulations
African (AFR)
AF:
AC:
40260
AN:
41546
American (AMR)
AF:
AC:
12924
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
AC:
3142
AN:
3472
East Asian (EAS)
AF:
AC:
3378
AN:
5170
South Asian (SAS)
AF:
AC:
3280
AN:
4820
European-Finnish (FIN)
AF:
AC:
7571
AN:
10582
Middle Eastern (MID)
AF:
AC:
269
AN:
294
European-Non Finnish (NFE)
AF:
AC:
56609
AN:
68008
Other (OTH)
AF:
AC:
1835
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
921
1842
2763
3684
4605
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
2459
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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