rs76863988

chr19-49664697-G-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001571.6(IRF3):c.142C>G(p.Gln48Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: IRF3 NM_001571.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140

Genes affected

IRF3 (HGNC:6118): (interferon regulatory factor 3) This gene encodes a member of the interferon regulatory transcription factor (IRF) family. The encoded protein is found in an inactive cytoplasmic form that upon serine/threonine phosphorylation forms a complex with CREBBP. This complex translocates to the nucleus and activates the transcription of interferons alpha and beta, as well as other interferon-induced genes. The protein plays an important role in the innate immune response against DNA and RNA viruses. Mutations in this gene are associated with Encephalopathy, acute, infection-induced, herpes-specific, 7. [provided by RefSeq, Sep 2020]

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.050522864).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IRF3	NM_001571.6	c.142C>G	p.Gln48Glu	missense_variant	2/8	ENST00000377139.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF3	ENST00000377139.8	c.142C>G	p.Gln48Glu	missense_variant	2/8	1	NM_001571.6	P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.068
BayesDel_addAF	Uncertain	0.022	T
BayesDel_noAF	Benign	-0.21
Cadd	Benign	10
Dann	Benign	0.68
DEOGEN2	Benign	0.41	T;.;.;T;T;.;T;T;T;.;.;.
Eigen	Benign	-1.5
Eigen_PC	Benign	-1.5
FATHMM_MKL	Benign	0.027	N
M_CAP	Benign	0.053	D
MetaRNN	Benign	0.051	T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	-0.11	T
MutationAssessor	Benign	0.39	N;.;N;N;N;N;.;.;.;.;N;.
MutationTaster	Benign	1.0	N;N;N;N
PrimateAI	Benign	0.26	T
PROVEAN	Benign	0.34	N;.;.;N;.;.;.;.;.;.;N;.
REVEL	Benign	0.27
Sift	Benign	0.97	T;.;.;T;.;.;.;.;.;.;T;.
Sift4G	Benign	0.72	T;T;T;T;T;T;.;T;.;.;T;.
Polyphen		0.0010	B;.;.;B;B;.;.;.;.;.;.;.
Vest4		0.13
MutPred		0.49		Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);Loss of MoRF binding (P = 0.0814);
MVP		0.87
MPC		0.41
ClinPred		0.13	T
GERP RS		-3.7
Varity_R		0.14
gMVP		0.14

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: rs76863988; hg19: chr19-50167954;