rs11269962

Variant names:

• chr7-128935743-TCTTAGCTATTGCTC-T
• rs11269962
• ENST00000898739.1:c.-12+2146_-12+2159delCTTAGCTATTGCTC

Your query was ambiguous. Multiple possible variants found:

• chr7-128935743-TCTTAGCTATTGCTC-T
• chr7-128935743-TCTTAGCTATTGCTC-TCTTAGCTATTGCTCCTTAGCTATTGCTC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000898739.1(IRF5):​c.-12+2146_-12+2159delCTTAGCTATTGCTC variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.38 (11600 hom., cov: 0)
• Consequence: IRF5 ENST00000898739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.612
• Publications: 2 publications found

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]

IRF5 Gene-Disease associations (from GenCC):

• systemic lupus erythematosus

  Inheritance: Unknown Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000898739.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IRF5	ENST00000898739.1		c.-12+2146_-12+2159delCTTAGCTATTGCTC		intron	N/A	ENSP00000568798.1

Frequencies

GnomAD3 genomes AF: 0.377 AC: 57271 AN: 151968 Hom.: 11602 Cov.: 0

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.402

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.417

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.377 AC: 57288 AN: 152086 Hom.: 11600 Cov.: 0 AF XY: 0.372 AC XY: 27678 AN XY: 74328

African (AFR) AF: 0.260 AC: 10783 AN: 41506

American (AMR) AF: 0.404 AC: 6183 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3468

East Asian (EAS) AF: 0.122 AC: 635 AN: 5188

South Asian (SAS) AF: 0.396 AC: 1910 AN: 4820

European-Finnish (FIN) AF: 0.402 AC: 4249 AN: 10578

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30280 AN: 67924

Other (OTH) AF: 0.415 AC: 876 AN: 2112

Alfa AF: 0.404 Hom.: 1550

Bravo AF: 0.373

Asia WGS AF: 0.236 AC: 822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.61

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs11269962; hg19: chr7-128575797;