chr3-184135073-A-G
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NR_183718.1(EIF2B5-DT):n.67+122T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 433,852 control chromosomes in the GnomAD database, including 16,017 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.29 ( 6793 hom., cov: 32)
Exomes 𝑓: 0.25 ( 9224 hom. )
Consequence
EIF2B5-DT
NR_183718.1 intron, non_coding_transcript
NR_183718.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.787
Genes affected
EIF2B5-DT (HGNC:55202): (EIF2B5 divergent transcript)
EIF2B5 (HGNC:3261): (eukaryotic translation initiation factor 2B subunit epsilon) 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, Nov 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=-0.8).
BP6
Variant 3-184135073-A-G is Benign according to our data. Variant chr3-184135073-A-G is described in ClinVar as [Benign]. Clinvar id is 344322.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EIF2B5-DT | NR_183718.1 | n.67+122T>C | intron_variant, non_coding_transcript_variant | ||||
EIF2B5-DT | NR_183721.1 | n.189T>C | non_coding_transcript_exon_variant | 1/2 | |||
EIF2B5-DT | NR_183719.1 | n.67+122T>C | intron_variant, non_coding_transcript_variant | ||||
EIF2B5-DT | NR_183720.1 | n.104+85T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EIF2B5-DT | ENST00000608135.1 | n.44+122T>C | intron_variant, non_coding_transcript_variant | 5 | |||||
EIF2B5 | ENST00000491144.5 | n.36A>G | non_coding_transcript_exon_variant | 1/15 | 2 | ||||
EIF2B5-DT | ENST00000608232.5 | n.24+85T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.289 AC: 43844AN: 151834Hom.: 6788 Cov.: 32
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GnomAD4 exome AF: 0.245 AC: 69067AN: 281900Hom.: 9224 Cov.: 0 AF XY: 0.245 AC XY: 36009AN XY: 147184
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GnomAD4 genome AF: 0.289 AC: 43889AN: 151952Hom.: 6793 Cov.: 32 AF XY: 0.294 AC XY: 21845AN XY: 74274
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Vanishing white matter disease Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at