Variant rs79606093 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001414.4(EIF2B1):c.483-22G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0287 in 1,613,684 control chromosomes in the GnomAD database, including 2,262 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.073 ( 1016 hom., cov: 32)

Exomes 𝑓: 0.024 ( 1246 hom. )

Consequence

EIF2B1
NM_001414.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -3.98

Variant links:

Genes affected

EIF2B1 (HGNC:3257): (eukaryotic translation initiation factor 2B subunit alpha) This gene encodes one of five subunits of eukaryotic translation initiation factor 2B (EIF2B), a GTP exchange factor for eukaryotic initiation factor 2 and an essential regulator for protein synthesis. Mutations in this gene and the genes encoding other EIF2B subunits have been associated with leukoencephalopathy with vanishing white matter. [provided by RefSeq, Oct 2009]

EIF2B1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 12-123626515-C-A is Benign according to our data. Variant chr12-123626515-C-A is described in ClinVar as [Benign]. Clinvar id is 258091.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
EIF2B1	NM_001414.4 linkuse as main transcript	c.483-22G>T		intron_variant		ENST00000424014.7	NP_001405.1	Q14232-1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
EIF2B1	ENST00000424014.7 linkuse as main transcript	c.483-22G>T	intron_variant		1	NM_001414.4	ENSP00000416250.2	Q14232-1
EIF2B1	ENST00000537073.1 linkuse as main transcript	c.*342G>T	3_prime_UTR_variant	5/5	2		ENSP00000444183.1	Q14232-2
EIF2B1	ENST00000539951.5 linkuse as main transcript	c.444-22G>T	intron_variant		5		ENSP00000438060.1	F5H0D0
EIF2B1	ENST00000534960.5 linkuse as main transcript	c.415-1653G>T	intron_variant		5		ENSP00000443172.1	H0YGG4

Frequencies

GnomAD3 genomes

AF:

0.0728

AC:

11064

AN:

152006

Hom.:

1005

Cov.:

show subpopulations

Gnomad AFR

AF:

0.217

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0350

Gnomad ASJ

AF:

0.0196

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0294

Gnomad FIN

AF:

0.00671

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0172

Gnomad OTH

AF:

0.0488

GnomAD3 exomes

AF:

0.0311

AC:

7807

AN:

251350

Hom.:

464

AF XY:

0.0285

AC XY:

3871

AN XY:

135854

show subpopulations

Gnomad AFR exome

AF:

0.227

Gnomad AMR exome

AF:

0.0173

Gnomad ASJ exome

AF:

0.0184

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0370

Gnomad FIN exome

AF:

0.00814

Gnomad NFE exome

AF:

0.0166

Gnomad OTH exome

AF:

0.0230

GnomAD4 exome

AF:

0.0241

AC:

35152

AN:

1461560

Hom.:

1246

Cov.:

AF XY:

0.0240

AC XY:

17438

AN XY:

727128

show subpopulations

Gnomad4 AFR exome

AF:

0.228

Gnomad4 AMR exome

AF:

0.0192

Gnomad4 ASJ exome

AF:

0.0192

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0388

Gnomad4 FIN exome

AF:

0.00861

Gnomad4 NFE exome

AF:

0.0182

Gnomad4 OTH exome

AF:

0.0314

GnomAD4 genome

AF:

0.0731

AC:

11115

AN:

152124

Hom.:

1016

Cov.:

AF XY:

0.0710

AC XY:

5283

AN XY:

74366

show subpopulations

Gnomad4 AFR

AF:

0.217

Gnomad4 AMR

AF:

0.0350

Gnomad4 ASJ

AF:

0.0196

Gnomad4 EAS

AF:

0.000386

Gnomad4 SAS

AF:

0.0292

Gnomad4 FIN

AF:

0.00671

Gnomad4 NFE

AF:

0.0173

Gnomad4 OTH

AF:

0.0488

Alfa

AF:

0.0358

Hom.:

Bravo

AF:

0.0821

Asia WGS

AF:

0.0300

AC:

104

AN:

3478

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

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.33

DANN

Benign

0.57

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

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