rs763645
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_021807.4(EXOC4):c.1514+28534C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,950 control chromosomes in the GnomAD database, including 14,854 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 0.43 ( 14854 hom., cov: 33)
Consequence
EXOC4
NM_021807.4 intron
NM_021807.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.861
Publications
3 publications found
Genes affected
EXOC4 (HGNC:30389): (exocyst complex component 4) The protein encoded by this gene is a component of the exocyst complex, a multiple protein complex essential for targeting exocytic vesicles to specific docking sites on the plasma membrane. Though best characterized in yeast, the component proteins and functions of exocyst complex have been demonstrated to be highly conserved in higher eukaryotes. At least eight components of the exocyst complex, including this protein, are found to interact with the actin cytoskeletal remodeling and vesicle transport machinery. The complex is also essential for the biogenesis of epithelial cell surface polarity. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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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=-0.92).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.428 AC: 64952AN: 151832Hom.: 14840 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
64952
AN:
151832
Hom.:
Cov.:
33
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: 0.428 AC: 64997AN: 151950Hom.: 14854 Cov.: 33 AF XY: 0.435 AC XY: 32302AN XY: 74232 show subpopulations
GnomAD4 genome
AF:
AC:
64997
AN:
151950
Hom.:
Cov.:
33
AF XY:
AC XY:
32302
AN XY:
74232
show subpopulations
African (AFR)
AF:
AC:
12210
AN:
41432
American (AMR)
AF:
AC:
8631
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
AC:
1742
AN:
3466
East Asian (EAS)
AF:
AC:
2816
AN:
5146
South Asian (SAS)
AF:
AC:
1441
AN:
4808
European-Finnish (FIN)
AF:
AC:
5946
AN:
10562
Middle Eastern (MID)
AF:
AC:
110
AN:
294
European-Non Finnish (NFE)
AF:
AC:
30774
AN:
67958
Other (OTH)
AF:
AC:
889
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1857
3714
5570
7427
9284
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
596
1192
1788
2384
2980
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1462
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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