11-613297-T-G

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001572.5(IRF7):c.1146A>C(p.Gly382Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,607,992 control chromosomes in the GnomAD database, including 64,358 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G382G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.33 ( 9387 hom., cov: 31)

Exomes 𝑓: 0.27 ( 54971 hom. )

Consequence

IRF7
NM_001572.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4O:1

Conservation

PhyloP100: -1.78

Publications

24 publications found

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 Gene-Disease associations (from GenCC):

immunodeficiency 39
Inheritance: AR Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

IRF7 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP6

Variant 11-613297-T-G is Benign according to our data. Variant chr11-613297-T-G is described in ClinVar as Benign. ClinVar VariationId is 1170387.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.78 with no splicing effect.

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.1146A>C	p.Gly382Gly	synonymous_variant	Exon 9 of 11	ENST00000525445.6	NP_001563.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IRF7	ENST00000525445.6 link	c.1146A>C	p.Gly382Gly	synonymous_variant	Exon 9 of 11	5	NM_001572.5	ENSP00000434009.2		Q92985-1

Frequencies

GnomAD3 genomes

AF:

0.326

AC:

49340

AN:

151520

Hom.:

9371

Cov.:

show subpopulations

Gnomad AFR

AF:

0.519

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.348

Gnomad EAS

AF:

0.0254

Gnomad SAS

AF:

0.129

Gnomad FIN

AF:

0.186

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.270

Gnomad OTH

AF:

0.333

GnomAD2 exomes

AF:

0.252

AC:

60036

AN:

237930

AF XY:

0.243

show subpopulations

Gnomad AFR exome

AF:

0.515

Gnomad AMR exome

AF:

0.325

Gnomad ASJ exome

AF:

0.333

Gnomad EAS exome

AF:

0.0284

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.260

GnomAD4 exome

AF:

0.265

AC:

386252

AN:

1456358

Hom.:

54971

Cov.:

AF XY:

0.261

AC XY:

188798

AN XY:

724230

show subpopulations

African (AFR)

AF:

0.522

AC:

17425

AN:

33384

American (AMR)

AF:

0.323

AC:

14217

AN:

44034

Ashkenazi Jewish (ASJ)

AF:

0.335

AC:

8684

AN:

25922

East Asian (EAS)

AF:

0.0229

AC:

905

AN:

39536

South Asian (SAS)

AF:

0.143

AC:

12276

AN:

85890

European-Finnish (FIN)

AF:

0.198

AC:

10210

AN:

51604

Middle Eastern (MID)

AF:

0.306

AC:

1753

AN:

5728

European-Non Finnish (NFE)

AF:

0.274

AC:

304376

AN:

1110098

Other (OTH)

AF:

0.273

AC:

16406

AN:

60162

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

16290

32580

48871

65161

81451

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10238

20476

30714

40952

51190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.326

AC:

49391

AN:

151634

Hom.:

9387

Cov.:

AF XY:

0.315

AC XY:

23339

AN XY:

74062

show subpopulations

African (AFR)

AF:

0.519

AC:

21478

AN:

41394

American (AMR)

AF:

0.307

AC:

4685

AN:

15248

Ashkenazi Jewish (ASJ)

AF:

0.348

AC:

1204

AN:

3464

East Asian (EAS)

AF:

0.0255

AC:

130

AN:

5108

South Asian (SAS)

AF:

0.128

AC:

612

AN:

4794

European-Finnish (FIN)

AF:

0.186

AC:

1963

AN:

10532

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.270

AC:

18334

AN:

67790

Other (OTH)

AF:

0.331

AC:

696

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

1621

3242

4863

6484

8105

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

458

916

1374

1832

2290

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.274

Hom.:

3812

Bravo

AF:

0.345

Asia WGS

AF:

0.126

AC:

438

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Immunodeficiency 39

Benign:2

Jul 14, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:1Other:1

GenomeConnect, ClinGen

Significance:not provided

Review Status:no classification provided

Collection Method:phenotyping only

Variant interpreted as Benign and reported on 04-27-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. This variant was reported in an individual referred for clinical diagnostic genetic testing. -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.1

(source)

DANN

Benign

0.76

PhyloP100

-1.8

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over