rs182503338

Positions:

• chr6-34614497-T-G

Variant summary

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

The NM_024294.4(ILRUN):​c.512-7593A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 135,466 control chromosomes in the GnomAD database, including 105 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 0.022 (105 hom., cov: 28)
• Consequence: ILRUN NM_024294.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.412

Genes affected

ILRUN (HGNC:21215): (inflammation and lipid regulator with UBA-like and NBR1-like domains) This gene encodes a protein with N-terminal ubiquitin-associated (UBA)-like and central neighbor of BRCA1 gene 1 (NBR1)-like domains. The protein acts an inhibitor of antiviral and proinflammatory cytokine transcription and as a regulator of the renin-angiotensin-aldosterone system (RAAS). [provided by RefSeq, Jul 2021]

ILRUN (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0642 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ILRUN	NM_024294.4	c.512-7593A>C		intron_variant		ENST00000374023.8	NP_077270.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ILRUN	ENST00000374023.8	c.512-7593A>C		intron_variant		1	NM_024294.4	ENSP00000363135.3
ILRUN	ENST00000374026.7	c.314-7593A>C		intron_variant		2		ENSP00000363138.3
ILRUN	ENST00000374021.1	c.290-7593A>C		intron_variant		3		ENSP00000363133.1

Frequencies

GnomAD3 genomes AF: 0.0221 AC: 2995 AN: 135478 Hom.: 105 Cov.: 28

Gnomad AFR AF: 0.0665

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0118

Gnomad ASJ AF: 0.00422

Gnomad EAS AF: 0.000394

Gnomad SAS AF: 0.0155

Gnomad FIN AF: 0.00338

Gnomad MID AF: 0.0238

Gnomad NFE AF: 0.00618

Gnomad OTH AF: 0.0241

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

GnomAD4 genome AF: 0.0221 AC: 2997 AN: 135466 Hom.: 105 Cov.: 28 AF XY: 0.0213 AC XY: 1398 AN XY: 65628

Gnomad4 AFR AF: 0.0665

Gnomad4 AMR AF: 0.0118

Gnomad4 ASJ AF: 0.00422

Gnomad4 EAS AF: 0.000395

Gnomad4 SAS AF: 0.0154

Gnomad4 FIN AF: 0.00338

Gnomad4 NFE AF: 0.00618

Gnomad4 OTH AF: 0.0240

Alfa AF: 0.0209 Hom.: 14

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs182503338; hg19: chr6-34582274;