rs205262

Positions:

• chr6-34595387-A-G

Variant summary

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

The NM_024294.4(ILRUN):​c.862-4787T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,128 control chromosomes in the GnomAD database, including 12,929 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 0.37 (12929 hom., cov: 33)
• Consequence: ILRUN NM_024294.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.693

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

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 = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ILRUN	NM_024294.4	c.862-4787T>C		intron_variant		ENST00000374023.8	NP_077270.1
ILRUN	NM_022758.6	c.664-4787T>C		intron_variant			NP_073595.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ILRUN	ENST00000374023.8	c.862-4787T>C		intron_variant		1	NM_024294.4	ENSP00000363135	P1
ILRUN	ENST00000374021.1	c.640-4787T>C		intron_variant		3		ENSP00000363133
ILRUN	ENST00000374026.7	c.664-4787T>C		intron_variant		2		ENSP00000363138

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56775 AN: 152010 Hom.: 12891 Cov.: 33

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.196

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.374 AC: 56860 AN: 152128 Hom.: 12929 Cov.: 33 AF XY: 0.371 AC XY: 27569 AN XY: 74392

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.297

Gnomad4 NFE AF: 0.278

Gnomad4 OTH AF: 0.370

Alfa AF: 0.294 Hom.: 10099

Bravo AF: 0.385

Asia WGS AF: 0.197 AC: 685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.78
DANN	Benign	0.59

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: rs205262; hg19: chr6-34563164;