7-128935498-C-G

Variant names:

• chr7-128935498-C-G
• rs3778754
• ENST00000898739.1:c.-12+1900C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000898739.1(IRF5):​c.-12+1900C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 152,144 control chromosomes in the GnomAD database, including 12,915 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 (12915 hom., cov: 33)
• Consequence: IRF5 ENST00000898739.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 20 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 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+1900C>G		intron	N/A	ENSP00000568798.1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 61034 AN: 152026 Hom.: 12915 Cov.: 33

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.401 AC: 61056 AN: 152144 Hom.: 12915 Cov.: 33 AF XY: 0.396 AC XY: 29457 AN XY: 74372

African (AFR) AF: 0.301 AC: 12489 AN: 41520

American (AMR) AF: 0.414 AC: 6328 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.582 AC: 2019 AN: 3470

East Asian (EAS) AF: 0.190 AC: 986 AN: 5182

South Asian (SAS) AF: 0.432 AC: 2087 AN: 4826

European-Finnish (FIN) AF: 0.406 AC: 4299 AN: 10584

Middle Eastern (MID) AF: 0.521 AC: 152 AN: 292

European-Non Finnish (NFE) AF: 0.461 AC: 31332 AN: 67970

Other (OTH) AF: 0.448 AC: 943 AN: 2106

Alfa AF: 0.415 Hom.: 1646

Bravo AF: 0.398

Asia WGS AF: 0.291 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.1
DANN	Benign	0.36
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs3778754; hg19: chr7-128575552;