12-123621091-G-A

Position:

• chr12-123621091-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001414.4(EIF2B1):​c.*665C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0739 in 155,120 control chromosomes in the GnomAD database, including 602 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.074 (599 hom., cov: 30)
  • Exomes 𝑓: 0.043 (3 hom.)
• Consequence: EIF2B1 NM_001414.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.299

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 12-123621091-G-A is Benign according to our data. Variant chr12-123621091-G-A is described in ClinVar as [Benign]. Clinvar id is 307515.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.137 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
EIF2B1	NM_001414.4	c.*665C>T		3_prime_UTR_variant	9/9	ENST00000424014.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
EIF2B1	ENST00000424014.7	c.*665C>T		3_prime_UTR_variant	9/9	1	NM_001414.4	P1

Frequencies

GnomAD3 genomes AF: 0.0743 AC: 11308 AN: 152100 Hom.: 592 Cov.: 30

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0369

Gnomad EAS AF: 0.0887

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0464

Gnomad OTH AF: 0.0653

GnomAD4 exome AF: 0.0434 AC: 126 AN: 2902 Hom.: 3 Cov.: 0 AF XY: 0.0435 AC XY: 64 AN XY: 1470

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0240

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.0577

Gnomad4 SAS exome AF: 0.105

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0427

Gnomad4 OTH exome AF: 0.0426

GnomAD4 genome AF: 0.0744 AC: 11331 AN: 152218 Hom.: 599 Cov.: 30 AF XY: 0.0740 AC XY: 5506 AN XY: 74436

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.0333

Gnomad4 ASJ AF: 0.0369

Gnomad4 EAS AF: 0.0879

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0464

Gnomad4 OTH AF: 0.0731

Alfa AF: 0.0458 Hom.: 93

Bravo AF: 0.0741

Asia WGS AF: 0.123 AC: 426 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

-

- -

Vanishing white matter disease Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	8.0
DANN	Benign	0.76
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.3

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

Other links and lift over

dbSNP: rs2707; hg19: chr12-124105638;