rs7536700

chr1-153668351-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004515.4(ILF2):c.213+102G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0912 in 1,399,308 control chromosomes in the GnomAD database, including 8,593 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 0.14 (2503 hom., cov: 32)
  • Exomes 𝑓: 0.085 (6090 hom.)
• Consequence: ILF2 NM_004515.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.69

Genes affected

ILF2 (HGNC:6037): (interleukin enhancer binding factor 2) The protein encoded by this gene is a transcription factor required for T-cell expression of the interleukin 2 gene. It also binds RNA and is an essential component for encapsidation and protein priming of hepatitis B viral polymerase. The encoded 45 kDa protein (NF45, ILF2) forms a complex with the 90 kDa interleukin enhancer-binding factor 3 (NF90, ILF3), and this complex has been shown to affect the redistribution of nuclear mRNA to the cytoplasm, to repair DNA breaks by nonhomologous end joining, and to negatively regulate the microRNA processing pathway. Knockdown of NF45 or NF90 protein retards cell growth, possibly by inhibition of mRNA stabilization. Alternative splicing results in multiple transcript variants. Related pseudogenes have been found on chromosomes 3 and 14. [provided by RefSeq, Dec 2014]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.313 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ILF2	NM_004515.4	c.213+102G>A		intron_variant		ENST00000361891.9
ILF2	NM_001267809.2	c.99+102G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ILF2	ENST00000361891.9	c.213+102G>A		intron_variant		1	NM_004515.4	P1
ILF2	ENST00000368681.1	c.213+102G>A		intron_variant		2
ILF2	ENST00000368684.8	c.99+102G>A		intron_variant		5
ILF2	ENST00000615950.4	c.99+102G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21970 AN: 152112 Hom.: 2488 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0146

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0701

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.0729

Gnomad OTH AF: 0.141

GnomAD4 exome AF: 0.0846 AC: 105534 AN: 1247078 Hom.: 6090 AF XY: 0.0861 AC XY: 53562 AN XY: 621782

Gnomad4 AFR exome AF: 0.329

Gnomad4 AMR exome AF: 0.0854

Gnomad4 ASJ exome AF: 0.146

Gnomad4 EAS exome AF: 0.0131

Gnomad4 SAS exome AF: 0.146

Gnomad4 FIN exome AF: 0.0649

Gnomad4 NFE exome AF: 0.0729

Gnomad4 OTH exome AF: 0.105

GnomAD4 genome AF: 0.145 AC: 22016 AN: 152230 Hom.: 2503 Cov.: 32 AF XY: 0.142 AC XY: 10587 AN XY: 74454

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0145

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0701

Gnomad4 NFE AF: 0.0730

Gnomad4 OTH AF: 0.141

Alfa AF: 0.0956 Hom.: 1241

Bravo AF: 0.153

Asia WGS AF: 0.105 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.24
Dann	Benign	0.41

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: rs7536700; hg19: chr1-153640827;