rs376350717

Variant names:

• chr11-614874-A-C
• NM_001572.5:c.317T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-614874-A-C
• chr11-614874-A-G
• chr11-614874-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001572.5(IRF7):​c.317T>G​(p.Val106Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000014 in 1,426,270 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 35)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: IRF7 NM_001572.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.205

Genes affected

IRF7 (HGNC:6122): (interferon regulatory factor 7) This gene encodes interferon regulatory factor 7, a member of the interferon regulatory transcription factor (IRF) family. It has been shown to play a role in the transcriptional activation of virus-inducible cellular genes, including interferon beta chain genes. Inducible expression of IRF7 is largely restricted to lymphoid tissue. The encoded protein plays an important role in the innate immune response against DNA and RNA viruses. [provided by RefSeq, Jul 2021]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.38201386).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IRF7	NM_001572.5	c.317T>G	p.Val106Gly	missense_variant	Exon 4 of 11	ENST00000525445.6	NP_001563.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRF7	ENST00000525445.6	c.317T>G	p.Val106Gly	missense_variant	Exon 4 of 11	5	NM_001572.5	ENSP00000434009.2

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome AF: 0.00000140 AC: 2 AN: 1426270 Hom.: 0 Cov.: 37 AF XY: 0.00000141 AC XY: 1 AN XY: 706910

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000182

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Uncertain	0.16	D
BayesDel_noAF	Uncertain	-0.010
CADD	Benign	17
DANN	Benign	0.64
DEOGEN2	Uncertain	0.72	D;.;.;D;D;.;.;.
Eigen	Benign	-0.44
Eigen_PC	Benign	-0.66
FATHMM_MKL	Benign	0.36	N
LIST_S2	Benign	0.67	.;T;T;T;T;.;T;T
M_CAP	Pathogenic	0.29	D
MetaRNN	Benign	0.38	T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.57	D
MutationAssessor	Uncertain	2.5	M;.;M;M;.;.;.;.
PrimateAI	Uncertain	0.56	T
PROVEAN	Uncertain	-3.5	D;D;D;.;.;D;.;.
REVEL	Uncertain	0.47
Sift	Uncertain	0.0090	D;D;D;.;.;D;.;.
Sift4G	Benign	0.41	T;T;T;.;T;T;.;.
Polyphen		1.0	D;D;D;D;.;D;.;.
Vest4		0.29
MutPred		0.44		Gain of disorder (P = 0.0195);.;Gain of disorder (P = 0.0195);Gain of disorder (P = 0.0195);.;.;Gain of disorder (P = 0.0195);.;
MVP		0.64
MPC		0.50
ClinPred		0.31	T
GERP RS		0.45
Varity_R		0.33
gMVP		0.53

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr11-614874;