NM_001003722.2:c.322-35_322-29delTTTTTTA
Variant summary
Our verdict is Benign. The variant received -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_001003722.2(GLE1):c.322-35_322-29delTTTTTTA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 1,162,682 control chromosomes in the GnomAD database, including 37,221 homozygotes. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.27 ( 6060 hom., cov: 21)
Exomes 𝑓: 0.24 ( 31161 hom. )
Consequence
GLE1
NM_001003722.2 intron
NM_001003722.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.45
Publications
0 publications found
Genes affected
GLE1 (HGNC:4315): (GLE1 RNA export mediator) This gene encodes a predicted 75-kDa polypeptide with high sequence and structure homology to yeast Gle1p, which is nuclear protein with a leucine-rich nuclear export sequence essential for poly(A)+RNA export. Inhibition of human GLE1L by microinjection of antibodies against GLE1L in HeLa cells resulted in inhibition of poly(A)+RNA export. Immunoflourescence studies show that GLE1L is localized at the nuclear pore complexes. This localization suggests that GLE1L may act at a terminal step in the export of mature RNA messages to the cytoplasm. Two alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
GLE1 Gene-Disease associations (from GenCC):
- lethal arthrogryposis-anterior horn cell disease syndromeInheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, G2P
- lethal congenital contracture syndrome 1Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)
- amyotrophic lateral sclerosisInheritance: AD Classification: SUPPORTIVE, LIMITED Submitted by: ClinGen, Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -16 ACMG points.
BP6
Variant 9-128515490-CTTATTTT-C is Benign according to our data. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr9-128515490-CTTATTTT-C is described in CliVar as Benign. Clinvar id is 256859.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.269 AC: 40783AN: 151498Hom.: 6049 Cov.: 21 show subpopulations
GnomAD3 genomes
AF:
AC:
40783
AN:
151498
Hom.:
Cov.:
21
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
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Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.283 AC: 59611AN: 210280 AF XY: 0.280 show subpopulations
GnomAD2 exomes
AF:
AC:
59611
AN:
210280
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.242 AC: 245122AN: 1011064Hom.: 31161 AF XY: 0.244 AC XY: 126919AN XY: 520328 show subpopulations
GnomAD4 exome
AF:
AC:
245122
AN:
1011064
Hom.:
AF XY:
AC XY:
126919
AN XY:
520328
show subpopulations
African (AFR)
AF:
AC:
9692
AN:
24552
American (AMR)
AF:
AC:
12823
AN:
41798
Ashkenazi Jewish (ASJ)
AF:
AC:
3912
AN:
22964
East Asian (EAS)
AF:
AC:
17734
AN:
36108
South Asian (SAS)
AF:
AC:
24087
AN:
74856
European-Finnish (FIN)
AF:
AC:
12128
AN:
50206
Middle Eastern (MID)
AF:
AC:
1263
AN:
4944
European-Non Finnish (NFE)
AF:
AC:
152157
AN:
710138
Other (OTH)
AF:
AC:
11326
AN:
45498
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
9844
19688
29532
39376
49220
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
4592
9184
13776
18368
22960
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.269 AC: 40826AN: 151618Hom.: 6060 Cov.: 21 AF XY: 0.274 AC XY: 20265AN XY: 74070 show subpopulations
GnomAD4 genome
AF:
AC:
40826
AN:
151618
Hom.:
Cov.:
21
AF XY:
AC XY:
20265
AN XY:
74070
show subpopulations
African (AFR)
AF:
AC:
15326
AN:
41248
American (AMR)
AF:
AC:
3889
AN:
15228
Ashkenazi Jewish (ASJ)
AF:
AC:
560
AN:
3468
East Asian (EAS)
AF:
AC:
2378
AN:
5136
South Asian (SAS)
AF:
AC:
1628
AN:
4800
European-Finnish (FIN)
AF:
AC:
2660
AN:
10534
Middle Eastern (MID)
AF:
AC:
69
AN:
290
European-Non Finnish (NFE)
AF:
AC:
13650
AN:
67900
Other (OTH)
AF:
AC:
531
AN:
2106
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.487
Heterozygous variant carriers
0
1414
2829
4243
5658
7072
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
416
832
1248
1664
2080
<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:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
-
PreventionGenetics, part of Exact Sciences
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
not provided Benign:1
May 26, 2021
GeneDx
Significance:Benign
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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