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GeneBe

rs2070197

Variant summary

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

The NM_001098629.3(IRF5):c.*128T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 1,201,678 control chromosomes in the GnomAD database, including 8,087 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 0.090 ( 862 hom., cov: 33)
Exomes 𝑓: 0.11 ( 7225 hom. )

Consequence

IRF5
NM_001098629.3 3_prime_UTR

Scores

2

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -0.862
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IRF5NM_001098629.3 linkuse as main transcriptc.*128T>C 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.*128T>C 3_prime_UTR_variant 9/91 NM_001098629.3 Q13568-2

Frequencies

GnomAD3 genomes
AF:
0.0904
AC:
13755
AN:
152100
Hom.:
865
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0244
Gnomad AMI
AF:
0.0373
Gnomad AMR
AF:
0.139
Gnomad ASJ
AF:
0.114
Gnomad EAS
AF:
0.00193
Gnomad SAS
AF:
0.153
Gnomad FIN
AF:
0.145
Gnomad MID
AF:
0.130
Gnomad NFE
AF:
0.113
Gnomad OTH
AF:
0.103
GnomAD4 exome
AF:
0.110
AC:
115067
AN:
1049460
Hom.:
7225
Cov.:
14
AF XY:
0.111
AC XY:
57904
AN XY:
522450
show subpopulations
Gnomad4 AFR exome
AF:
0.0189
Gnomad4 AMR exome
AF:
0.191
Gnomad4 ASJ exome
AF:
0.113
Gnomad4 EAS exome
AF:
0.000253
Gnomad4 SAS exome
AF:
0.157
Gnomad4 FIN exome
AF:
0.152
Gnomad4 NFE exome
AF:
0.109
Gnomad4 OTH exome
AF:
0.108
GnomAD4 genome
AF:
0.0903
AC:
13749
AN:
152218
Hom.:
862
Cov.:
33
AF XY:
0.0930
AC XY:
6922
AN XY:
74438
show subpopulations
Gnomad4 AFR
AF:
0.0243
Gnomad4 AMR
AF:
0.139
Gnomad4 ASJ
AF:
0.114
Gnomad4 EAS
AF:
0.00193
Gnomad4 SAS
AF:
0.154
Gnomad4 FIN
AF:
0.145
Gnomad4 NFE
AF:
0.113
Gnomad4 OTH
AF:
0.102
Alfa
AF:
0.101
Hom.:
138
Bravo
AF:
0.0870
Asia WGS
AF:
0.0580
AC:
202
AN:
3478

ClinVar

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

Submissions by phenotype

Systemic lupus erythematosus, association with susceptibility to, 10 Other:1
risk factor, no assertion criteria providedliterature onlyOMIMJul 01, 2007- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
Cadd
Benign
4.8
Dann
Benign
0.40

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: rs2070197; hg19: chr7-128589000; COSMIC: COSV50857256; COSMIC: COSV50857256; API