rs7298287
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001414.4(EIF2B1):c.370-20A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0909 in 1,603,222 control chromosomes in the GnomAD database, including 13,539 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.19 ( 5082 hom., cov: 32)
Exomes 𝑓: 0.081 ( 8457 hom. )
Consequence
EIF2B1
NM_001414.4 intron
NM_001414.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.54
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 12-123627176-T-C is Benign according to our data. Variant chr12-123627176-T-C is described in ClinVar as [Benign]. Clinvar id is 93731.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2B1 | NM_001414.4 | c.370-20A>G | intron_variant | ENST00000424014.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2B1 | ENST00000424014.7 | c.370-20A>G | intron_variant | 1 | NM_001414.4 | P1 | |||
EIF2B1 | ENST00000534960.5 | c.417-2314A>G | intron_variant | 5 | |||||
EIF2B1 | ENST00000537073.1 | c.370-20A>G | intron_variant | 2 | |||||
EIF2B1 | ENST00000539951.5 | c.331-20A>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.186 AC: 28208AN: 151924Hom.: 5036 Cov.: 32
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GnomAD3 exomes AF: 0.108 AC: 27245AN: 251366Hom.: 2912 AF XY: 0.103 AC XY: 14026AN XY: 135866
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GnomAD4 exome AF: 0.0809 AC: 117442AN: 1451180Hom.: 8457 Cov.: 28 AF XY: 0.0822 AC XY: 59389AN XY: 722584
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GnomAD4 genome ? AF: 0.186 AC: 28316AN: 152042Hom.: 5082 Cov.: 32 AF XY: 0.184 AC XY: 13654AN XY: 74328
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 09, 2012 | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at