rs1874328

Variant summary

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

The NM_001098629.3(IRF5):​c.196-795A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 152,094 control chromosomes in the GnomAD database, including 12,064 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 0.40 ( 12064 hom., cov: 32)

Consequence

IRF5
NM_001098629.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.435
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=-0.93).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
IRF5NM_001098629.3 linkuse as main transcriptc.196-795A>G intron_variant ENST00000357234.10

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
IRF5ENST00000357234.10 linkuse as main transcriptc.196-795A>G intron_variant 1 NM_001098629.3 Q13568-2

Frequencies

GnomAD3 genomes
AF:
0.395
AC:
60022
AN:
151976
Hom.:
12049
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.451
Gnomad AMI
AF:
0.402
Gnomad AMR
AF:
0.317
Gnomad ASJ
AF:
0.514
Gnomad EAS
AF:
0.391
Gnomad SAS
AF:
0.357
Gnomad FIN
AF:
0.354
Gnomad MID
AF:
0.399
Gnomad NFE
AF:
0.381
Gnomad OTH
AF:
0.400
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.395
AC:
60082
AN:
152094
Hom.:
12064
Cov.:
32
AF XY:
0.389
AC XY:
28902
AN XY:
74368
show subpopulations
Gnomad4 AFR
AF:
0.452
Gnomad4 AMR
AF:
0.316
Gnomad4 ASJ
AF:
0.514
Gnomad4 EAS
AF:
0.392
Gnomad4 SAS
AF:
0.357
Gnomad4 FIN
AF:
0.354
Gnomad4 NFE
AF:
0.381
Gnomad4 OTH
AF:
0.400
Alfa
AF:
0.390
Hom.:
20248
Bravo
AF:
0.398
Asia WGS
AF:
0.388
AC:
1351
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.93
CADD
Benign
1.2
DANN
Benign
0.28

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: rs1874328; hg19: chr7-128585104; API