rs2549007

chr5-132491183-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000680796.1(IRF1):c.-5-1700A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.605 in 151,628 control chromosomes in the GnomAD database, including 28,383 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 0.60 (28383 hom., cov: 34)
• Consequence: IRF1 ENST00000680796.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

Genes affected

IRF1 (HGNC:6116): (interferon regulatory factor 1) The protein encoded by this gene is a transcriptional regulator and tumor suppressor, serving as an activator of genes involved in both innate and acquired immune responses. The encoded protein activates the transcription of genes involved in the body's response to viruses and bacteria, playing a role in cell proliferation, apoptosis, the immune response, and DNA damage response. This protein represses the transcription of several other genes. As a tumor suppressor, it both suppresses tumor cell growth and stimulates an immune response against tumor cells. Defects in this gene have been associated with gastric cancer, myelogenous leukemia, and lung cancer. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.661 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IRF1	ENST00000680796.1	c.-5-1700A>G		intron_variant
IRF1	ENST00000681584.1	c.-5-1700A>G		intron_variant
IRF1	ENST00000463784.6	n.30+171A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.605 AC: 91658 AN: 151510 Hom.: 28364 Cov.: 34

Gnomad AFR AF: 0.460

Gnomad AMI AF: 0.771

Gnomad AMR AF: 0.651

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.668

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.605 AC: 91720 AN: 151628 Hom.: 28383 Cov.: 34 AF XY: 0.607 AC XY: 44937 AN XY: 74066

Gnomad4 AFR AF: 0.460

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.637

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.668

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.629

Alfa AF: 0.627 Hom.: 3743

Bravo AF: 0.600

Asia WGS AF: 0.619 AC: 2149 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	9.9
Dann	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2549007; hg19: chr5-131826875; COSMIC: COSV55376700; COSMIC: COSV55376700;