3-37248331-C-T

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.84

Publications

5 publications found
Variant links:
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]

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=-0.98).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.961 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GOLGA4NM_002078.5 linkc.73-3064C>T intron_variant Intron 1 of 23 ENST00000361924.7 NP_002069.2 Q13439-1Q49A56

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GOLGA4ENST00000361924.7 linkc.73-3064C>T intron_variant Intron 1 of 23 1 NM_002078.5 ENSP00000354486.2 Q13439-1

Frequencies

GnomAD3 genomes
AF:
0.854
AC:
129919
AN:
152092
Hom.:
56174
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.969
Gnomad AMI
AF:
0.830
Gnomad AMR
AF:
0.845
Gnomad ASJ
AF:
0.905
Gnomad EAS
AF:
0.653
Gnomad SAS
AF:
0.681
Gnomad FIN
AF:
0.715
Gnomad MID
AF:
0.924
Gnomad NFE
AF:
0.832
Gnomad OTH
AF:
0.871
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.854
AC:
130025
AN:
152210
Hom.:
56219
Cov.:
31
AF XY:
0.847
AC XY:
63011
AN XY:
74426
show subpopulations
African (AFR)
AF:
0.969
AC:
40260
AN:
41546
American (AMR)
AF:
0.845
AC:
12924
AN:
15294
Ashkenazi Jewish (ASJ)
AF:
0.905
AC:
3142
AN:
3472
East Asian (EAS)
AF:
0.653
AC:
3378
AN:
5170
South Asian (SAS)
AF:
0.680
AC:
3280
AN:
4820
European-Finnish (FIN)
AF:
0.715
AC:
7571
AN:
10582
Middle Eastern (MID)
AF:
0.915
AC:
269
AN:
294
European-Non Finnish (NFE)
AF:
0.832
AC:
56609
AN:
68008
Other (OTH)
AF:
0.869
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

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
884
1768
2652
3536
4420
<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:
0.847
Hom.:
171061
Bravo
AF:
0.871
Asia WGS
AF:
0.707
AC:
2459
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.98
CADD
Benign
0.065
DANN
Benign
0.23
PhyloP100
-1.8
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

Publications

Other links and lift over

dbSNP: rs336597; hg19: chr3-37289822; API