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

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.802

Links

IRF5 (HGNC:6120):

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
IRF5	NM_001098629.3 linkuse as main transcript	c.-12+198T>G		intron_variant		ENST00000357234.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF5	ENST00000357234.10 linkuse as main transcript	c.-12+198T>G		intron_variant		1	NM_001098629.3		Q13568-2

Frequencies

GnomAD3 genomes

AF:

0.526

AC:

79628

AN:

151418

Hom.:

21275

Cov.:

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.:

AF XY:

0.549

AC XY:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over