Variant chr1-32229218-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_003757.4(EIF3I):c.803+10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0835 in 1,609,044 control chromosomes in the GnomAD database, including 7,764 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.096 ( 899 hom., cov: 32)

Exomes 𝑓: 0.082 ( 6865 hom. )

Consequence

EIF3I
NM_003757.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 0.355

Variant links:

Genes affected

EIF3I (HGNC:3272): (eukaryotic translation initiation factor 3 subunit I) Contributes to translation initiation factor activity. Involved in translational initiation. Located in extracellular exosome. Part of eukaryotic translation initiation factor 3 complex. [provided by Alliance of Genome Resources, Apr 2022]

EIF3I links:

EIF3I (HGNC:):

EIF3I links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BP6

Variant 1-32229218-A-G is Benign according to our data. Variant chr1-32229218-A-G is described in ClinVar as [Benign]. Clinvar id is 1327736.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
EIF3I	NM_003757.4 linkuse as main transcript	c.803+10A>G	intron_variant	ENST00000677711.2	NP_003748.1	Q13347Q5U0F4
EIF3I	NM_001394168.1 linkuse as main transcript	c.803+10A>G	intron_variant		NP_001381097.1
EIF3I	XM_024450518.2 linkuse as main transcript	c.404+10A>G	intron_variant		XP_024306286.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
EIF3I	ENST00000677711.2 linkuse as main transcript	c.803+10A>G		intron_variant			NM_003757.4	ENSP00000504061.1		Q13347

Frequencies

GnomAD3 genomes

AF:

0.0961

AC:

14610

AN:

152074

Hom.:

893

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0959

Gnomad AMI

AF:

0.0877

Gnomad AMR

AF:

0.141

Gnomad ASJ

AF:

0.0689

Gnomad EAS

AF:

0.235

Gnomad SAS

AF:

0.252

Gnomad FIN

AF:

0.101

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0655

Gnomad OTH

AF:

0.0932

GnomAD3 exomes

AF:

0.112

AC:

27655

AN:

246292

Hom.:

2188

AF XY:

0.115

AC XY:

15286

AN XY:

133424

show subpopulations

Gnomad AFR exome

AF:

0.0986

Gnomad AMR exome

AF:

0.137

Gnomad ASJ exome

AF:

0.0691

Gnomad EAS exome

AF:

0.246

Gnomad SAS exome

AF:

0.234

Gnomad FIN exome

AF:

0.103

Gnomad NFE exome

AF:

0.0602

Gnomad OTH exome

AF:

0.0837

GnomAD4 exome

AF:

0.0822

AC:

119762

AN:

1456852

Hom.:

6865

Cov.:

AF XY:

0.0861

AC XY:

62382

AN XY:

724932

show subpopulations

Gnomad4 AFR exome

AF:

0.103

Gnomad4 AMR exome

AF:

0.139

Gnomad4 ASJ exome

AF:

0.0680

Gnomad4 EAS exome

AF:

0.213

Gnomad4 SAS exome

AF:

0.229

Gnomad4 FIN exome

AF:

0.0972

Gnomad4 NFE exome

AF:

0.0628

Gnomad4 OTH exome

AF:

0.0896

GnomAD4 genome

AF:

0.0961

AC:

14629

AN:

152192

Hom.:

899

Cov.:

AF XY:

0.102

AC XY:

7569

AN XY:

74390

show subpopulations

Gnomad4 AFR

AF:

0.0958

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.0689

Gnomad4 EAS

AF:

0.235

Gnomad4 SAS

AF:

0.252

Gnomad4 FIN

AF:

0.101

Gnomad4 NFE

AF:

0.0654

Gnomad4 OTH

AF:

0.0922

Alfa

AF:

0.0735

Hom.:

173

Bravo

AF:

0.0948

Asia WGS

AF:

0.248

AC:

861

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 10, 2021	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

3.3

DANN

Benign

0.89

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over