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GeneBe

1-44894615-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_020365.5(EIF2B3):c.656+2740A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 151,930 control chromosomes in the GnomAD database, including 15,024 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 ( 15024 hom., cov: 31)

Consequence

EIF2B3
NM_020365.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.00
Variant links:
Genes affected
EIF2B3 (HGNC:3259): (eukaryotic translation initiation factor 2B subunit gamma) The protein encoded by this gene is one of the subunits of initiation factor eIF2B, which catalyzes the exchange of eukaryotic initiation factor 2-bound GDP for GTP. It has also been found to function as a cofactor of hepatitis C virus internal ribosome entry site-mediated translation. Mutations in this gene have been associated with leukodystrophy with vanishing white matter. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
EIF2B3NM_020365.5 linkuse as main transcriptc.656+2740A>C intron_variant ENST00000360403.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
EIF2B3ENST00000360403.7 linkuse as main transcriptc.656+2740A>C intron_variant 1 NM_020365.5 P1Q9NR50-1
EIF2B3ENST00000372183.7 linkuse as main transcriptc.656+2740A>C intron_variant 1 Q9NR50-2
EIF2B3ENST00000620860.4 linkuse as main transcriptc.656+2740A>C intron_variant 1 Q9NR50-3
EIF2B3ENST00000439363.5 linkuse as main transcriptc.118+2740A>C intron_variant 3

Frequencies

GnomAD3 genomes
AF:
0.431
AC:
65417
AN:
151812
Hom.:
14989
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.590
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.467
Gnomad ASJ
AF:
0.321
Gnomad EAS
AF:
0.446
Gnomad SAS
AF:
0.343
Gnomad FIN
AF:
0.338
Gnomad MID
AF:
0.234
Gnomad NFE
AF:
0.356
Gnomad OTH
AF:
0.382
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.431
AC:
65507
AN:
151930
Hom.:
15024
Cov.:
31
AF XY:
0.430
AC XY:
31928
AN XY:
74276
show subpopulations
Gnomad4 AFR
AF:
0.590
Gnomad4 AMR
AF:
0.468
Gnomad4 ASJ
AF:
0.321
Gnomad4 EAS
AF:
0.446
Gnomad4 SAS
AF:
0.343
Gnomad4 FIN
AF:
0.338
Gnomad4 NFE
AF:
0.356
Gnomad4 OTH
AF:
0.378
Alfa
AF:
0.414
Hom.:
2756
Bravo
AF:
0.449
Asia WGS
AF:
0.380
AC:
1321
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
Cadd
Benign
2.6
Dann
Benign
0.84

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.

Other links and lift over

dbSNP: rs263977; hg19: chr1-45360287; API