1-153668351-C-T

Variant names:

• chr1-153668351-C-T
• rs7536700
• NM_004515.4:c.213+102G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004515.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ILF2	NM_004515.4	MANE Select	c.213+102G>A		intron	N/A	NP_004506.2
	ILF2	NM_001267809.2		c.99+102G>A		intron	N/A	NP_001254738.1	B4DY09

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ILF2	ENST00000361891.9	TSL:1 MANE Select	c.213+102G>A		intron	N/A	ENSP00000355011.4	Q12905
	ILF2	ENST00000911670.1		c.213+102G>A		intron	N/A	ENSP00000581729.1
	ILF2	ENST00000903918.1		c.213+102G>A		intron	N/A	ENSP00000573977.1

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

African (AFR) AF: 0.329 AC: 9164 AN: 27838

American (AMR) AF: 0.0854 AC: 2756 AN: 32256

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 3413 AN: 23398

East Asian (EAS) AF: 0.0131 AC: 469 AN: 35894

South Asian (SAS) AF: 0.146 AC: 10827 AN: 74148

European-Finnish (FIN) AF: 0.0649 AC: 3244 AN: 50018

Middle Eastern (MID) AF: 0.222 AC: 1184 AN: 5332

European-Non Finnish (NFE) AF: 0.0729 AC: 68958 AN: 945454

Other (OTH) AF: 0.105 AC: 5519 AN: 52740

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

African (AFR) AF: 0.317 AC: 13165 AN: 41512

American (AMR) AF: 0.102 AC: 1560 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 457 AN: 3466

East Asian (EAS) AF: 0.0145 AC: 75 AN: 5188

South Asian (SAS) AF: 0.140 AC: 675 AN: 4822

European-Finnish (FIN) AF: 0.0701 AC: 744 AN: 10620

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4962 AN: 68018

Other (OTH) AF: 0.141 AC: 299 AN: 2114

Alfa AF: 0.104 Hom.: 3912

Bravo AF: 0.153

Asia WGS AF: 0.105 AC: 368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.24
DANN	Benign	0.41
PhyloP100		-1.7
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7536700; hg19: chr1-153640827;