Variant 11-613165-G-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001572.5(IRF7):c.1237+41C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 1,601,674 control chromosomes in the GnomAD database, including 63,684 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 9384 hom., cov: 32)

Exomes 𝑓: 0.26 ( 54300 hom. )

Consequence

IRF7
NM_001572.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: 0.299

Variant links:

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]

IRF7 links:

IRF7 (HGNC:):

IRF7 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 11-613165-G-C is Benign according to our data. Variant chr11-613165-G-C is described in ClinVar as [Benign]. Clinvar id is 1185464.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.512 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IRF7	NM_001572.5 linkuse as main transcript	c.1237+41C>G		intron_variant		ENST00000525445.6	NP_001563.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IRF7	ENST00000525445.6 linkuse as main transcript	c.1237+41C>G		intron_variant		5	NM_001572.5	ENSP00000434009.2		Q92985-1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49363

AN:

152050

Hom.:

9368

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.306

Gnomad ASJ

AF:

0.346

Gnomad EAS

AF:

0.0251

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.185

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.332

GnomAD3 exomes

AF:

0.250

AC:

60151

AN:

240300

Hom.:

8870

AF XY:

0.240

AC XY:

31369

AN XY:

130754

show subpopulations

Gnomad AFR exome

AF:

0.519

Gnomad AMR exome

AF:

0.319

Gnomad ASJ exome

AF:

0.336

Gnomad EAS exome

AF:

0.0280

Gnomad SAS exome

AF:

0.140

Gnomad FIN exome

AF:

0.187

Gnomad NFE exome

AF:

0.263

Gnomad OTH exome

AF:

0.257

GnomAD4 exome

AF:

0.264

AC:

383172

AN:

1449506

Hom.:

54300

Cov.:

AF XY:

0.260

AC XY:

186952

AN XY:

719916

show subpopulations

Gnomad4 AFR exome

AF:

0.522

Gnomad4 AMR exome

AF:

0.319

Gnomad4 ASJ exome

AF:

0.335

Gnomad4 EAS exome

AF:

0.0228

Gnomad4 SAS exome

AF:

0.142

Gnomad4 FIN exome

AF:

0.198

Gnomad4 NFE exome

AF:

0.273

Gnomad4 OTH exome

AF:

0.271

GnomAD4 genome

AF:

0.325

AC:

49414

AN:

152168

Hom.:

9384

Cov.:

AF XY:

0.314

AC XY:

23352

AN XY:

74402

show subpopulations

Gnomad4 AFR

AF:

0.518

Gnomad4 AMR

AF:

0.307

Gnomad4 ASJ

AF:

0.346

Gnomad4 EAS

AF:

0.0251

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.270

Gnomad4 OTH

AF:

0.330

Alfa

AF:

0.308

Hom.:

1416

Bravo

AF:

0.345

Asia WGS

AF:

0.126

AC:

439

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

This variant is classified as Benign based on local population frequency. This variant was detected in 59% of patients studied by a panel of primary immunodeficiencies. Number of patients: 56. Only high quality variants are reported. -

Immunodeficiency 39

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 14, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

1.1

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over