Variant chr9-128515490-CTTATTTT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001003722.2(GLE1):c.322-35_322-29del 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

Scores

Not classified

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.45

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 9-128515490-CTTATTTT-C is Benign according to our data. Variant chr9-128515490-CTTATTTT-C is described in ClinVar 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

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GLE1	NM_001003722.2 linkuse as main transcript	c.322-35_322-29del		intron_variant		ENST00000309971.9	NP_001003722.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GLE1	ENST00000309971.9 linkuse as main transcript	c.322-35_322-29del		intron_variant		1	NM_001003722.2	ENSP00000308622	P1	Q53GS7-1

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40783

AN:

151498

Hom.:

6049

Cov.:

show subpopulations

Gnomad AFR

AF:

0.372

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.256

Gnomad ASJ

AF:

0.161

Gnomad EAS

AF:

0.463

Gnomad SAS

AF:

0.338

Gnomad FIN

AF:

0.253

Gnomad MID

AF:

0.232

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.252

GnomAD3 exomes

AF:

0.283

AC:

59611

AN:

210280

Hom.:

8637

AF XY:

0.280

AC XY:

32073

AN XY:

114352

show subpopulations

Gnomad AFR exome

AF:

0.422

Gnomad AMR exome

AF:

0.316

Gnomad ASJ exome

AF:

0.175

Gnomad EAS exome

AF:

0.464

Gnomad SAS exome

AF:

0.331

Gnomad FIN exome

AF:

0.255

Gnomad NFE exome

AF:

0.228

Gnomad OTH exome

AF:

0.247

GnomAD4 exome

AF:

0.242

AC:

245122

AN:

1011064

Hom.:

31161

AF XY:

0.244

AC XY:

126919

AN XY:

520328

show subpopulations

Gnomad4 AFR exome

AF:

0.395

Gnomad4 AMR exome

AF:

0.307

Gnomad4 ASJ exome

AF:

0.170

Gnomad4 EAS exome

AF:

0.491

Gnomad4 SAS exome

AF:

0.322

Gnomad4 FIN exome

AF:

0.242

Gnomad4 NFE exome

AF:

0.214

Gnomad4 OTH exome

AF:

0.249

GnomAD4 genome

AF:

0.269

AC:

40826

AN:

151618

Hom.:

6060

Cov.:

AF XY:

0.274

AC XY:

20265

AN XY:

74070

show subpopulations

Gnomad4 AFR

AF:

0.372

Gnomad4 AMR

AF:

0.255

Gnomad4 ASJ

AF:

0.161

Gnomad4 EAS

AF:

0.463

Gnomad4 SAS

AF:

0.339

Gnomad4 FIN

AF:

0.253

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.252

Alfa

AF:

0.223

Hom.:

754

Bravo

AF:

0.279

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 26, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over