dbSNP rs12422022: IRF7:c.1237+14T>C (chr11-613192-A-G) – ACMG Classification: Benign (-20 pts)

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+14T>C 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 1,588,768 control chromosomes in the GnomAD database, including 63,222 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 9399 hom., cov: 32)

Exomes 𝑓: 0.26 ( 53823 hom. )

Consequence

IRF7
NM_001572.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -0.621

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:

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=-0.91).

BP6

Variant 11-613192-A-G is Benign according to our data. Variant chr11-613192-A-G is described in ClinVar as [Benign]. Clinvar id is 1166881.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IRF7	NM_001572.5 link	c.1237+14T>C		intron_variant	Intron 9 of 10	ENST00000525445.6	NP_001563.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRF7	ENST00000525445.6 link	c.1237+14T>C		intron_variant	Intron 9 of 10	5	NM_001572.5	ENSP00000434009.2		Q92985-1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49397

AN:

152038

Hom.:

9383

Cov.:

show subpopulations

Gnomad AFR

AF:

0.519

Gnomad AMI

AF:

0.208

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.0254

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:

0.248

AC:

57295

AN:

230658

Hom.:

8369

AF XY:

0.238

AC XY:

30001

AN XY:

125872

show subpopulations

Gnomad AFR exome

AF:

0.513

Gnomad AMR exome

AF:

0.318

Gnomad ASJ exome

AF:

0.334

Gnomad EAS exome

AF:

0.0277

Gnomad SAS exome

AF:

0.139

Gnomad FIN exome

AF:

0.186

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.258

GnomAD4 exome

AF:

0.264

AC:

379724

AN:

1436612

Hom.:

53823

Cov.:

AF XY:

0.260

AC XY:

184920

AN XY:

712180

show subpopulations

Gnomad4 AFR exome

AF:

0.522

Gnomad4 AMR exome

AF:

0.316

Gnomad4 ASJ exome

AF:

0.334

Gnomad4 EAS exome

AF:

0.0228

Gnomad4 SAS exome

AF:

0.142

Gnomad4 FIN exome

AF:

0.198

Gnomad4 NFE exome

AF:

0.274

Gnomad4 OTH exome

AF:

0.272

GnomAD4 genome

AF:

0.325

AC:

49448

AN:

152156

Hom.:

9399

Cov.:

AF XY:

0.314

AC XY:

23370

AN XY:

74410

show subpopulations

Gnomad4 AFR

AF:

0.518

Gnomad4 AMR

AF:

0.307

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.0255

Gnomad4 SAS

AF:

0.127

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:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Immunodeficiency 39

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified

Benign:1

Jan 24, 2024

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.4

DANN

Benign

0.32

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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