6-34613859-T-G

Position:

• chr6-34613859-T-G

Variant summary

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

The ENST00000374023.8(ILRUN):​c.512-6955A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,062 control chromosomes in the GnomAD database, including 2,295 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 0.17 (2295 hom., cov: 31)
• Consequence: ILRUN ENST00000374023.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.222 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ILRUN	NM_024294.4	c.512-6955A>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.512-6955A>C		intron_variant		1	NM_024294.4	ENSP00000363135	P1
ILRUN	ENST00000374021.1	c.290-6955A>C		intron_variant		3		ENSP00000363133
ILRUN	ENST00000374026.7	c.314-6955A>C		intron_variant		2		ENSP00000363138

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25202 AN: 151944 Hom.: 2293 Cov.: 31

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0114

Gnomad SAS AF: 0.0810

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.166 AC: 25221 AN: 152062 Hom.: 2295 Cov.: 31 AF XY: 0.167 AC XY: 12399 AN XY: 74322

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0114

Gnomad4 SAS AF: 0.0798

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.149

Gnomad4 OTH AF: 0.156

Alfa AF: 0.174 Hom.: 363

Bravo AF: 0.163

Asia WGS AF: 0.0460 AC: 162 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.81

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2744971; hg19: chr6-34581636;