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GeneBe

rs2004640

Variant summary

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

The NM_001098629.3(IRF5):c.-12+198T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,736 control chromosomes in the GnomAD database, including 21,339 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.53 ( 21302 hom., cov: 32)
Exomes 𝑓: 0.56 ( 37 hom. )

Consequence

IRF5
NM_001098629.3 intron

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.802
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=-0.79).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IRF5NM_001098629.3 linkuse as main transcriptc.-12+198T>G intron_variant ENST00000357234.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IRF5ENST00000357234.10 linkuse as main transcriptc.-12+198T>G intron_variant 1 NM_001098629.3 Q13568-2

Frequencies

GnomAD3 genomes
AF:
0.526
AC:
79628
AN:
151418
Hom.:
21275
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.584
Gnomad AMI
AF:
0.510
Gnomad AMR
AF:
0.542
Gnomad ASJ
AF:
0.384
Gnomad EAS
AF:
0.721
Gnomad SAS
AF:
0.494
Gnomad FIN
AF:
0.485
Gnomad MID
AF:
0.376
Gnomad NFE
AF:
0.490
Gnomad OTH
AF:
0.491
GnomAD4 exome
AF:
0.559
AC:
113
AN:
202
Hom.:
37
Cov.:
0
AF XY:
0.549
AC XY:
89
AN XY:
162
show subpopulations
Gnomad4 AFR exome
AF:
0.750
Gnomad4 EAS exome
AF:
0.833
Gnomad4 SAS exome
AF:
0.750
Gnomad4 NFE exome
AF:
0.547
Gnomad4 OTH exome
AF:
0.375
GnomAD4 genome
AF:
0.526
AC:
79705
AN:
151534
Hom.:
21302
Cov.:
32
AF XY:
0.529
AC XY:
39171
AN XY:
74052
show subpopulations
Gnomad4 AFR
AF:
0.584
Gnomad4 AMR
AF:
0.543
Gnomad4 ASJ
AF:
0.384
Gnomad4 EAS
AF:
0.720
Gnomad4 SAS
AF:
0.493
Gnomad4 FIN
AF:
0.485
Gnomad4 NFE
AF:
0.490
Gnomad4 OTH
AF:
0.494
Alfa
AF:
0.377
Hom.:
1334
Bravo
AF:
0.531

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.79
Cadd
Benign
5.9

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: rs2004640; hg19: chr7-128578301; API