dbSNP rs2569507: ILF3:c.2435-322G>A (chr19-10688228-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_017620.3(ILF3):c.2435-322G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 275,726 control chromosomes in the GnomAD database, including 29,225 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.44 ( 15429 hom., cov: 32)

Exomes 𝑓: 0.46 ( 13796 hom. )

Consequence

ILF3
NM_017620.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.21

Publications

14 publications found

Variant links:

Genes affected

ILF3 (HGNC:6038): (interleukin enhancer binding factor 3) This gene encodes a double-stranded RNA (dsRNA) binding protein that complexes with other proteins, dsRNAs, small noncoding RNAs, and mRNAs to regulate gene expression and stabilize mRNAs. This protein (NF90, ILF3) forms a heterodimer with a 45 kDa transcription factor (NF45, ILF2) required for T-cell expression of interleukin 2. This complex has been shown to affect the redistribution of nuclear mRNA to the cytoplasm. Knockdown of NF45 or NF90 protein retards cell growth, possibly by inhibition of mRNA stabilization. In contrast, an isoform (NF110) of this gene that is predominantly restricted to the nucleus has only minor effects on cell growth when its levels are reduced. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Dec 2014]

ILF3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ILF3	NM_017620.3 link	c.2435-322G>A		intron_variant	Intron 18 of 19	ENST00000588657.6	NP_060090.2	Q12906-7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ILF3	ENST00000588657.6 link	c.2435-322G>A		intron_variant	Intron 18 of 19	5	NM_017620.3	ENSP00000468181.1		Q12906-7

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66729

AN:

151828

Hom.:

15430

Cov.:

show subpopulations

Gnomad AFR

AF:

0.301

Gnomad AMI

AF:

0.413

Gnomad AMR

AF:

0.517

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.318

Gnomad SAS

AF:

0.563

Gnomad FIN

AF:

0.455

Gnomad MID

AF:

0.382

Gnomad NFE

AF:

0.502

Gnomad OTH

AF:

0.435

GnomAD4 exome

AF:

0.462

AC:

57171

AN:

123778

Hom.:

13796

AF XY:

0.464

AC XY:

29031

AN XY:

62534

show subpopulations

African (AFR)

AF:

0.283

AC:

1165

AN:

4110

American (AMR)

AF:

0.539

AC:

2634

AN:

4888

Ashkenazi Jewish (ASJ)

AF:

0.507

AC:

2511

AN:

4954

East Asian (EAS)

AF:

0.246

AC:

2514

AN:

10210

South Asian (SAS)

AF:

0.536

AC:

1374

AN:

2562

European-Finnish (FIN)

AF:

0.462

AC:

3619

AN:

7838

Middle Eastern (MID)

AF:

0.405

AC:

276

AN:

682

European-Non Finnish (NFE)

AF:

0.488

AC:

39112

AN:

80074

Other (OTH)

AF:

0.469

AC:

3966

AN:

8460

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1451

2902

4353

5804

7255

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

224

448

672

896

1120

<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:

0.439

AC:

66725

AN:

151948

Hom.:

15429

Cov.:

AF XY:

0.440

AC XY:

32710

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.300

AC:

12411

AN:

41412

American (AMR)

AF:

0.517

AC:

7905

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.502

AC:

1742

AN:

3468

East Asian (EAS)

AF:

0.317

AC:

1640

AN:

5168

South Asian (SAS)

AF:

0.564

AC:

2718

AN:

4818

European-Finnish (FIN)

AF:

0.455

AC:

4802

AN:

10552

Middle Eastern (MID)

AF:

0.371

AC:

109

AN:

294

European-Non Finnish (NFE)

AF:

0.502

AC:

34104

AN:

67936

Other (OTH)

AF:

0.436

AC:

921

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1871

3743

5614

7486

9357

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.473

Hom.:

18140

Bravo

AF:

0.431

Asia WGS

AF:

0.469

AC:

1630

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.44

(source)

DANN

Benign

0.27

PhyloP100

-3.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over