7-128937860-C-CGCGGG

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001347928.2(IRF5):​c.-12+608_-12+612dupGGGGC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.37 ( 11067 hom., cov: 0)
Exomes 𝑓: 0.12 ( 1 hom. )

Consequence

IRF5
NM_001347928.2 intron

Scores

Not classified

Clinical Significance

risk factor no assertion criteria provided O:2

Conservation

PhyloP100: 0.213
Variant links:
Genes affected
IRF5 (HGNC:6120): (interferon regulatory factor 5) This gene encodes a member of the interferon regulatory factor (IRF) family, a group of transcription factors with diverse roles, including virus-mediated activation of interferon, and modulation of cell growth, differentiation, apoptosis, and immune system activity. Members of the IRF family are characterized by a conserved N-terminal DNA-binding domain containing tryptophan (W) repeats. Alternative promoter use and alternative splicing result in multiple transcript variants, and a 30-nt indel polymorphism (SNP rs60344245) can result in loss of a 10-aa segment. [provided by RefSeq, Dec 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
IRF5NM_001098629.3 linkc.-201_-200insGCGGG upstream_gene_variant ENST00000357234.10 NP_001092099.1 Q13568-2B7Z1M2C9JAU6

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
IRF5ENST00000357234.10 linkc.-201_-200insGCGGG upstream_gene_variant 1 NM_001098629.3 ENSP00000349770.5 Q13568-2

Frequencies

GnomAD3 genomes
AF:
0.370
AC:
55249
AN:
149364
Hom.:
11074
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.249
Gnomad AMI
AF:
0.452
Gnomad AMR
AF:
0.401
Gnomad ASJ
AF:
0.521
Gnomad EAS
AF:
0.121
Gnomad SAS
AF:
0.387
Gnomad FIN
AF:
0.383
Gnomad MID
AF:
0.490
Gnomad NFE
AF:
0.442
Gnomad OTH
AF:
0.409
GnomAD4 exome
AF:
0.117
AC:
11
AN:
94
Hom.:
1
Cov.:
0
AF XY:
0.0946
AC XY:
7
AN XY:
74
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.132
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.370
AC:
55242
AN:
149474
Hom.:
11067
Cov.:
0
AF XY:
0.364
AC XY:
26566
AN XY:
72896
show subpopulations
Gnomad4 AFR
AF:
0.249
Gnomad4 AMR
AF:
0.400
Gnomad4 ASJ
AF:
0.521
Gnomad4 EAS
AF:
0.121
Gnomad4 SAS
AF:
0.387
Gnomad4 FIN
AF:
0.383
Gnomad4 NFE
AF:
0.442
Gnomad4 OTH
AF:
0.407

ClinVar

Significance: risk factor
Submissions summary: Other:2
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Inflammatory bowel disease 14, susceptibility to Other:1
Mar 15, 2008
OMIM
Significance: risk factor
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Systemic lupus erythematosus, susceptibility to, 10 Other:1
Mar 15, 2008
OMIM
Significance: risk factor
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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.

Other links and lift over

dbSNP: rs77571059; hg19: chr7-128577914; API