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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(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 151418 control chromosomes in the gnomAD Genomes database, including 21275 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 ( 21275 hom., cov: 32)

Consequence

IRF5
NM_001098629 intron

Scores

1

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.802

Links

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
?
GnomAd 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
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
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
7.4

Splicing

Find out SpliceAI 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;