rs182503338

Variant names:

• chr6-34614497-T-G
• rs182503338
• NM_024294.4:c.512-7593A>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024294.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ILRUN	NM_024294.4	MANE Select	c.512-7593A>C		intron	N/A	NP_077270.1
	ILRUN	NM_022758.6		c.314-7593A>C		intron	N/A	NP_073595.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ILRUN	ENST00000374023.8	TSL:1 MANE Select	c.512-7593A>C		intron	N/A	ENSP00000363135.3
	ILRUN	ENST00000857869.1		c.596-7593A>C		intron	N/A	ENSP00000527928.1
	ILRUN	ENST00000857871.1		c.512-7593A>C		intron	N/A	ENSP00000527930.1

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

African (AFR) AF: 0.0665 AC: 2276 AN: 34216

American (AMR) AF: 0.0118 AC: 162 AN: 13782

Ashkenazi Jewish (ASJ) AF: 0.00422 AC: 14 AN: 3320

East Asian (EAS) AF: 0.000395 AC: 2 AN: 5058

South Asian (SAS) AF: 0.0154 AC: 71 AN: 4618

European-Finnish (FIN) AF: 0.00338 AC: 25 AN: 7402

Middle Eastern (MID) AF: 0.0261 AC: 7 AN: 268

European-Non Finnish (NFE) AF: 0.00618 AC: 396 AN: 64092

Other (OTH) AF: 0.0240 AC: 44 AN: 1836

Alfa AF: 0.0209 Hom.: 14

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.3
DANN	Benign	0.57
PhyloP100		0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs182503338; hg19: chr6-34582274;