Genetic Variant IRF7:c.1356+32T>C (chr11-612967-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.1356+32T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.271 in 1,605,328 control chromosomes in the GnomAD database, including 64,206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.33 ( 9395 hom., cov: 32)

Exomes 𝑓: 0.27 ( 54811 hom. )

Consequence

IRF7
NM_001572.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -1.64

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 11-612967-A-G is Benign according to our data. Variant chr11-612967-A-G is described in ClinVar as [Benign]. Clinvar id is 1185463.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.1356+32T>C		intron_variant	Intron 10 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.1356+32T>C		intron_variant	Intron 10 of 10	5	NM_001572.5	ENSP00000434009.2		Q92985-1

Frequencies

GnomAD3 genomes

AF:

0.325

AC:

49370

AN:

151908

Hom.:

9379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.519

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.307

Gnomad ASJ

AF:

0.347

Gnomad EAS

AF:

0.0255

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:

0.254

AC:

63399

AN:

249288

Hom.:

9651

AF XY:

0.244

AC XY:

32903

AN XY:

134994

show subpopulations

Gnomad AFR exome

AF:

0.523

Gnomad AMR exome

AF:

0.324

Gnomad ASJ exome

AF:

0.335

Gnomad EAS exome

AF:

0.0283

Gnomad SAS exome

AF:

0.140

Gnomad FIN exome

AF:

0.188

Gnomad NFE exome

AF:

0.268

Gnomad OTH exome

AF:

0.260

GnomAD4 exome

AF:

0.265

AC:

385219

AN:

1453304

Hom.:

54811

Cov.:

AF XY:

0.260

AC XY:

188365

AN XY:

723276

show subpopulations

Gnomad4 AFR exome

AF:

0.522

Gnomad4 AMR exome

AF:

0.321

Gnomad4 ASJ exome

AF:

0.335

Gnomad4 EAS exome

AF:

0.0228

Gnomad4 SAS exome

AF:

0.143

Gnomad4 FIN exome

AF:

0.199

Gnomad4 NFE exome

AF:

0.274

Gnomad4 OTH exome

AF:

0.273

GnomAD4 genome

AF:

0.325

AC:

49421

AN:

152024

Hom.:

9395

Cov.:

AF XY:

0.314

AC XY:

23357

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.519

Gnomad4 AMR

AF:

0.307

Gnomad4 ASJ

AF:

0.347

Gnomad4 EAS

AF:

0.0255

Gnomad4 SAS

AF:

0.128

Gnomad4 FIN

AF:

0.185

Gnomad4 NFE

AF:

0.270

Gnomad4 OTH

AF:

0.330

Alfa

AF:

0.289

Hom.:

6770

Bravo

AF:

0.345

Asia WGS

AF:

0.125

AC:

437

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

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. -

Immunodeficiency 39

Benign:1

Jul 14, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

-0.97

CADD

Benign

0.43

DANN

Benign

0.43

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

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