rs10954213

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001098629.3(IRF5):​c.*555G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 152,430 control chromosomes in the GnomAD database, including 25,782 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.58 ( 25754 hom., cov: 34)
Exomes 𝑓: 0.50 ( 28 hom. )

Consequence

IRF5
NM_001098629.3 3_prime_UTR

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: 1.53
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 -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IRF5NM_001098629.3 linkuse as main transcriptc.*555G>A 3_prime_UTR_variant 9/9 ENST00000357234.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IRF5ENST00000357234.10 linkuse as main transcriptc.*555G>A 3_prime_UTR_variant 9/91 NM_001098629.3 Q13568-2

Frequencies

GnomAD3 genomes
AF:
0.579
AC:
87999
AN:
152102
Hom.:
25745
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.529
Gnomad AMI
AF:
0.636
Gnomad AMR
AF:
0.525
Gnomad ASJ
AF:
0.720
Gnomad EAS
AF:
0.475
Gnomad SAS
AF:
0.616
Gnomad FIN
AF:
0.620
Gnomad MID
AF:
0.598
Gnomad NFE
AF:
0.611
Gnomad OTH
AF:
0.598
GnomAD4 exome
AF:
0.500
AC:
105
AN:
210
Hom.:
28
Cov.:
0
AF XY:
0.510
AC XY:
52
AN XY:
102
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.500
Gnomad4 EAS exome
AF:
1.00
Gnomad4 SAS exome
AF:
0.500
Gnomad4 NFE exome
AF:
0.505
Gnomad4 OTH exome
AF:
0.250
GnomAD4 genome
AF:
0.578
AC:
88047
AN:
152220
Hom.:
25754
Cov.:
34
AF XY:
0.576
AC XY:
42895
AN XY:
74414
show subpopulations
Gnomad4 AFR
AF:
0.529
Gnomad4 AMR
AF:
0.524
Gnomad4 ASJ
AF:
0.720
Gnomad4 EAS
AF:
0.475
Gnomad4 SAS
AF:
0.616
Gnomad4 FIN
AF:
0.620
Gnomad4 NFE
AF:
0.611
Gnomad4 OTH
AF:
0.595
Alfa
AF:
0.599
Hom.:
10738
Bravo
AF:
0.571
Asia WGS
AF:
0.527
AC:
1834
AN:
3476

ClinVar

Significance: risk factor
Submissions summary: Other:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Systemic lupus erythematosus, susceptibility to, 10 Other:1
risk factor, no assertion criteria providedliterature onlyOMIMMar 15, 2008- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Benign
10
DANN
Benign
0.74

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.

Other links and lift over

dbSNP: rs10954213; hg19: chr7-128589427; API