Genetic Variant EIF3B:c.-126_-124dupGGC (chr7-2354793-C-CGCG) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

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

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.362

Publications

0 publications found

Variant links:

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]

EIF3B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001362792.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EIF3B	NM_001362792.2		c.-504-438_-504-436dupGGC	intron	N/A	NP_001349721.1
EIF3B	NM_001362793.2		c.-504-438_-504-436dupGGC	intron	N/A	NP_001349722.1
EIF3B	NM_001037283.2	MANE Select	c.-129_-128insGCG	upstream_gene	N/A	NP_001032360.1	P55884-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
EIF3B	ENST00000922848.1		c.-126_-124dupGGC	5_prime_UTR	Exon 2 of 20	ENSP00000592907.1
EIF3B	ENST00000922849.1		c.-126_-124dupGGC	5_prime_UTR	Exon 1 of 19	ENSP00000592908.1
EIF3B	ENST00000431643.5	TSL:5	c.-504-438_-504-436dupGGC	intron	N/A	ENSP00000408062.1	C9JQN7

Frequencies

GnomAD3 genomes

AF:

0.274

AC:

41571

AN:

151690

Hom.:

5790

Cov.:

show subpopulations

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

show subpopulations

African (AFR)

AF:

0.274

AC:

4101

AN:

14944

American (AMR)

AF:

0.176

AC:

391

AN:

2226

Ashkenazi Jewish (ASJ)

AF:

0.228

AC:

1308

AN:

5748

East Asian (EAS)

AF:

0.252

AC:

1706

AN:

6778

South Asian (SAS)

AF:

0.393

AC:

5847

AN:

14878

European-Finnish (FIN)

AF:

0.331

AC:

1705

AN:

5152

Middle Eastern (MID)

AF:

0.233

AC:

395

AN:

1696

European-Non Finnish (NFE)

AF:

0.248

AC:

174877

AN:

704676

Other (OTH)

AF:

0.259

AC:

6929

AN:

26754

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.488

Heterozygous variant carriers

6571

13143

19714

26286

32857

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7906

15812

23718

31624

39530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.274

AC:

41630

AN:

151810

Hom.:

5804

Cov.:

AF XY:

0.280

AC XY:

20788

AN XY:

74222

show subpopulations

African (AFR)

AF:

0.278

AC:

11535

AN:

41454

American (AMR)

AF:

0.213

AC:

3254

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.246

AC:

852

AN:

3466

East Asian (EAS)

AF:

0.290

AC:

1484

AN:

5118

South Asian (SAS)

AF:

0.412

AC:

1983

AN:

4814

European-Finnish (FIN)

AF:

0.367

AC:

3862

AN:

10522

Middle Eastern (MID)

AF:

0.209

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.263

AC:

17880

AN:

67860

Other (OTH)

AF:

0.274

AC:

577

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

1546

3092

4638

6184

7730

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.278

Hom.:

638

Bravo

AF:

0.258

Asia WGS

AF:

0.381

AC:

1321

AN:

3468

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.36

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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7-2354793-CGCG-CGCGGCG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over