rs565147927
Variant summary
Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS1
The NM_004836.7(EIF2AK3):c.*870_*875delATGTTT variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.000138 in 152,366 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)
Consequence
EIF2AK3
NM_004836.7 3_prime_UTR
NM_004836.7 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 6.79
Publications
0 publications found
Genes affected
EIF2AK3 (HGNC:3255): (eukaryotic translation initiation factor 2 alpha kinase 3) The protein encoded by this gene phosphorylates the alpha subunit of eukaryotic translation-initiation factor 2, leading to its inactivation, and thus to a rapid reduction of translational initiation and repression of global protein synthesis. This protein is thought to modulate mitochondrial function. It is a type I membrane protein located in the endoplasmic reticulum (ER), where it is induced by ER stress caused by malfolded proteins. Mutations in this gene are associated with Wolcott-Rallison syndrome. [provided by RefSeq, Sep 2015]
EIF2AK3 Gene-Disease associations (from GenCC):
- Wolcott-Rallison syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, Genomics England PanelApp, G2P
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -4 ACMG points.
BS1
Variant frequency is greater than expected in population sas. GnomAd4 allele frequency = 0.000138 (21/152366) while in subpopulation SAS AF = 0.00414 (20/4832). AF 95% confidence interval is 0.00274. There are 0 homozygotes in GnomAd4. There are 12 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.000138 AC: 21AN: 152248Hom.: 0 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
21
AN:
152248
Hom.:
Cov.:
32
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 0.000138 AC: 21AN: 152366Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74512 show subpopulations
GnomAD4 genome
AF:
AC:
21
AN:
152366
Hom.:
Cov.:
32
AF XY:
AC XY:
12
AN XY:
74512
show subpopulations
African (AFR)
AF:
AC:
0
AN:
41590
American (AMR)
AF:
AC:
1
AN:
15300
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3470
East Asian (EAS)
AF:
AC:
0
AN:
5190
South Asian (SAS)
AF:
AC:
20
AN:
4832
European-Finnish (FIN)
AF:
AC:
0
AN:
10624
Middle Eastern (MID)
AF:
AC:
0
AN:
294
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68038
Other (OTH)
AF:
AC:
0
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.508
Heterozygous variant carriers
0
1
3
4
6
7
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Wolcott-Rallison dysplasia Uncertain:1
Jun 14, 2016
Illumina Laboratory Services, Illumina
Significance:Uncertain significance
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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