rs10954213

Variant summary

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

The NM_001098629(IRF5):c.*555G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.579 in 152102 control chromosomes in the gnomAD Genomes database, including 25745 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 0.58 ( 25745 hom., cov: 34)

Consequence

IRF5
NM_001098629 3_prime_UTR

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: 1.53

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=-0.5).

BA1

GnomAd highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.598 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.*555G>A		3_prime_UTR_variant	9/9	ENST00000357234.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF5	ENST00000357234.10 linkuse as main transcript	c.*555G>A		3_prime_UTR_variant	9/9	1	NM_001098629.3		Q13568-2

Frequencies

GnomAD3 genomes

AF:

0.579

AC:

87999

AN:

152102

Hom.:

25745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.529

Gnomad AMI

AF:

0.636

Gnomad AMR

AF:

0.525

Gnomad ASJ

AF:

0.720

Gnomad EAS

AF:

0.475

Gnomad SAS

AF:

0.616

Gnomad FIN

AF:

0.620

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.611

Gnomad OTH

AF:

0.598

GnomAD4 exome

AF:

0.500

AC:

105

AN:

210

Hom.:

AF XY:

0.510

AC XY:

AN XY:

102

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.500

Gnomad4 EAS exome

AF:

1.00

Gnomad4 SAS exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.505

Gnomad4 OTH exome

AF:

0.250

Alfa

AF:

0.599

Hom.:

10738

Bravo

AF:

0.571

Asia WGS

AF:

0.527

AC:

1834

AN:

3476

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Systemic lupus erythematosus, susceptibility to, 10

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Mar 15, 2008

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.50

Cadd

Benign

Dann

Benign

0.74

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over