Genetic Variant IRF8:c.-229_-220delGGCTGCAGGT (chr16-85902783-TGGTGGCTGCA-T) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_002163.4(IRF8):c.-1-228_-1-219delGGCTGCAGGT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

IRF8
NM_002163.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.378

Publications

0 publications found

Variant links:

Genes affected

IRF8 (HGNC:5358): (interferon regulatory factor 8) Interferon consensus sequence-binding protein (ICSBP) is a transcription factor of the interferon (IFN) regulatory factor (IRF) family. Proteins of this family are composed of a conserved DNA-binding domain in the N-terminal region and a divergent C-terminal region that serves as the regulatory domain. The IRF family proteins bind to the IFN-stimulated response element (ISRE) and regulate expression of genes stimulated by type I IFNs, namely IFN-alpha and IFN-beta. IRF family proteins also control expression of IFN-alpha and IFN-beta-regulated genes that are induced by viral infection. [provided by RefSeq, Jul 2008]

IRF8 Gene-Disease associations (from GenCC):

Mendelian susceptibility to mycobacterial diseases due to partial IRF8 deficiency
Inheritance: AD Classification: STRONG, SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, Illumina
immunodeficiency 32B
Inheritance: AR Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Ambry Genetics

IRF8 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
IRF8	NM_002163.4 link	c.-1-228_-1-219delGGCTGCAGGT	intron_variant	Intron 1 of 8	ENST00000268638.10	NP_002154.1	Q02556
IRF8	XM_047434052.1 link	c.-74_-65delGGCTGCAGGT	5_prime_UTR_variant	Exon 2 of 10		XP_047290008.1
IRF8	NM_001363907.1 link	c.-77_-68delGGTGGCTGCA	upstream_gene_variant			NP_001350836.1
IRF8	NM_001363908.1 link	c.-738_-729delGGTGGCTGCA	upstream_gene_variant			NP_001350837.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRF8	ENST00000268638.10 link	c.-1-228_-1-219delGGCTGCAGGT		intron_variant	Intron 1 of 8	1	NM_002163.4	ENSP00000268638.4		Q02556

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

416516

Hom.:

AF XY:

0.00

AC XY:

AN XY:

221838

African (AFR)

AF:

0.00

AC:

AN:

11838

American (AMR)

AF:

0.00

AC:

AN:

21054

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

13128

East Asian (EAS)

AF:

0.00

AC:

AN:

26626

South Asian (SAS)

AF:

0.00

AC:

AN:

47090

European-Finnish (FIN)

AF:

0.00

AC:

AN:

24316

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1800

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

246916

Other (OTH)

AF:

0.00

AC:

AN:

23748

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.38

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over