Variant chr5-132486174-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002198.3(IRF1):c.667+77A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 1,569,128 control chromosomes in the GnomAD database, including 94,812 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.38 ( 11295 hom., cov: 31)

Exomes 𝑓: 0.34 ( 83517 hom. )

Consequence

IRF1
NM_002198.3 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0520

Variant links:

Genes affected

IRF1 (HGNC:6116): (interferon regulatory factor 1) The protein encoded by this gene is a transcriptional regulator and tumor suppressor, serving as an activator of genes involved in both innate and acquired immune responses. The encoded protein activates the transcription of genes involved in the body's response to viruses and bacteria, playing a role in cell proliferation, apoptosis, the immune response, and DNA damage response. This protein represses the transcription of several other genes. As a tumor suppressor, it both suppresses tumor cell growth and stimulates an immune response against tumor cells. Defects in this gene have been associated with gastric cancer, myelogenous leukemia, and lung cancer. [provided by RefSeq, Aug 2017]

IRF1 links:

IRF1-AS1 (HGNC:33838): (colitis associated IRF1 antisense regulator of intestinal homeostasis)

IRF1-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 5-132486174-T-G is Benign according to our data. Variant chr5-132486174-T-G is described in ClinVar as [Benign]. Clinvar id is 2688385.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.482 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IRF1	NM_002198.3 linkuse as main transcript	c.667+77A>C		intron_variant		ENST00000245414.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF1	ENST00000245414.9 linkuse as main transcript	c.667+77A>C		intron_variant		1	NM_002198.3	P1
IRF1-AS1	ENST00000612967.2 linkuse as main transcript	n.281-18T>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.379

AC:

57516

AN:

151704

Hom.:

11281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.487

Gnomad AMI

AF:

0.226

Gnomad AMR

AF:

0.343

Gnomad ASJ

AF:

0.323

Gnomad EAS

AF:

0.362

Gnomad SAS

AF:

0.409

Gnomad FIN

AF:

0.330

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.333

Gnomad OTH

AF:

0.360

GnomAD3 exomes

AF:

0.348

AC:

83187

AN:

239334

Hom.:

14719

AF XY:

0.347

AC XY:

45029

AN XY:

129806

show subpopulations

Gnomad AFR exome

AF:

0.488

Gnomad AMR exome

AF:

0.326

Gnomad ASJ exome

AF:

0.313

Gnomad EAS exome

AF:

0.345

Gnomad SAS exome

AF:

0.389

Gnomad FIN exome

AF:

0.324

Gnomad NFE exome

AF:

0.330

Gnomad OTH exome

AF:

0.354

GnomAD4 exome

AF:

0.341

AC:

482912

AN:

1417306

Hom.:

83517

Cov.:

AF XY:

0.342

AC XY:

240278

AN XY:

703456

show subpopulations

Gnomad4 AFR exome

AF:

0.491

Gnomad4 AMR exome

AF:

0.330

Gnomad4 ASJ exome

AF:

0.314

Gnomad4 EAS exome

AF:

0.330

Gnomad4 SAS exome

AF:

0.386

Gnomad4 FIN exome

AF:

0.328

Gnomad4 NFE exome

AF:

0.334

Gnomad4 OTH exome

AF:

0.348

GnomAD4 genome

AF:

0.379

AC:

57573

AN:

151822

Hom.:

11295

Cov.:

AF XY:

0.378

AC XY:

28073

AN XY:

74186

show subpopulations

Gnomad4 AFR

AF:

0.487

Gnomad4 AMR

AF:

0.343

Gnomad4 ASJ

AF:

0.323

Gnomad4 EAS

AF:

0.361

Gnomad4 SAS

AF:

0.410

Gnomad4 FIN

AF:

0.330

Gnomad4 NFE

AF:

0.333

Gnomad4 OTH

AF:

0.360

Alfa

AF:

0.349

Hom.:

2088

Bravo

AF:

0.382

Asia WGS

AF:

0.377

AC:

1312

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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 65% of patients studied by a panel of primary immunodeficiencies. Number of patients: 57. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

7.0

DANN

Benign

0.63

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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