chr5-132492133-C-G

Variant summary

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

The ENST00000680796.1(IRF1):​c.-5-2650G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,056 control chromosomes in the GnomAD database, including 28,754 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 0.61 ( 28754 hom., cov: 32)

Consequence

IRF1
ENST00000680796.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.122
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.99).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.663 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
IRF1ENST00000680796.1 linkuse as main transcriptc.-5-2650G>C intron_variant ENSP00000506572
IRF1ENST00000681584.1 linkuse as main transcriptc.-5-2650G>C intron_variant ENSP00000505448

Frequencies

GnomAD3 genomes
AF:
0.608
AC:
92405
AN:
151938
Hom.:
28736
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.465
Gnomad AMI
AF:
0.772
Gnomad AMR
AF:
0.652
Gnomad ASJ
AF:
0.681
Gnomad EAS
AF:
0.638
Gnomad SAS
AF:
0.591
Gnomad FIN
AF:
0.670
Gnomad MID
AF:
0.503
Gnomad NFE
AF:
0.668
Gnomad OTH
AF:
0.632
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.608
AC:
92466
AN:
152056
Hom.:
28754
Cov.:
32
AF XY:
0.610
AC XY:
45328
AN XY:
74314
show subpopulations
Gnomad4 AFR
AF:
0.465
Gnomad4 AMR
AF:
0.652
Gnomad4 ASJ
AF:
0.681
Gnomad4 EAS
AF:
0.638
Gnomad4 SAS
AF:
0.591
Gnomad4 FIN
AF:
0.670
Gnomad4 NFE
AF:
0.668
Gnomad4 OTH
AF:
0.632
Alfa
AF:
0.524
Hom.:
1539
Bravo
AF:
0.602
Asia WGS
AF:
0.621
AC:
2157
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
7.9
DANN
Benign
0.63

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.

Other links and lift over

dbSNP: rs2549004; hg19: chr5-131827825; COSMIC: COSV55376727; COSMIC: COSV55376727; API