chr7-2354793-C-CGCG

Variant names:

• chr7-2354793-C-CGCG
• rs3216988
• XM_011515599.2:c.-126_-124dupGGC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001362792.2(EIF3B):​c.-504-438_-504-436dupGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 934,662 control chromosomes in the GnomAD database, including 31,717 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.27 (5804 hom., cov: 19)
  • Exomes 𝑓: 0.25 (25913 hom.)
• Consequence: EIF3B NM_001362792.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.362

Genes affected

EIF3B (HGNC:3280): (eukaryotic translation initiation factor 3 subunit B) Enables RNA binding activity. Contributes to translation initiation factor activity. Involved in several processes, including IRES-dependent viral translational initiation; translational initiation; and viral translational termination-reinitiation. Located in extracellular exosome. Part of eukaryotic translation initiation factor 3 complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-2354793-C-CGCG is Benign according to our data. Variant chr7-2354793-C-CGCG is described in ClinVar as [Benign]. Clinvar id is 1248882.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
EIF3B	NM_001037283.2	c.-129_-128insGCG		upstream_gene_variant		ENST00000360876.9	NP_001032360.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
EIF3B	ENST00000431643.5	c.-504-441_-504-440insGCG		intron_variant	Intron 1 of 7	5		ENSP00000408062.1
EIF3B	ENST00000360876.9	c.-129_-128insGCG		upstream_gene_variant		1	NM_001037283.2	ENSP00000354125.4
EIF3B	ENST00000397011.2	c.-129_-128insGCG		upstream_gene_variant		1		ENSP00000380206.2
EIF3B	ENST00000413917.5	c.-129_-128insGCG		upstream_gene_variant		2		ENSP00000407785.1

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41571 AN: 151690 Hom.: 5790 Cov.: 19

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.291

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.268

GnomAD4 exome AF: 0.252 AC: 197259 AN: 782852 Hom.: 25913 AF XY: 0.253 AC XY: 92822 AN XY: 366918

Gnomad4 AFR exome AF: 0.274

Gnomad4 AMR exome AF: 0.176

Gnomad4 ASJ exome AF: 0.228

Gnomad4 EAS exome AF: 0.252

Gnomad4 SAS exome AF: 0.393

Gnomad4 FIN exome AF: 0.331

Gnomad4 NFE exome AF: 0.248

Gnomad4 OTH exome AF: 0.259

GnomAD4 genome AF: 0.274 AC: 41630 AN: 151810 Hom.: 5804 Cov.: 19 AF XY: 0.280 AC XY: 20788 AN XY: 74222

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.274

Alfa AF: 0.278 Hom.: 638

Bravo AF: 0.258

Asia WGS AF: 0.381 AC: 1321 AN: 3468

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

May 21, 2021

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3216988; hg19: chr7-2394428;