rs2744971

Variant names:

• chr6-34613859-T-A
• rs2744971
• NM_024294.4:c.512-6955A>T

Your query was ambiguous. Multiple possible variants found:

• chr6-34613859-T-A
• chr6-34613859-T-C
• chr6-34613859-T-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_024294.4(ILRUN):​c.512-6955A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
• Consequence: ILRUN NM_024294.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.51
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ILRUN	NM_024294.4	MANE Select	c.512-6955A>T		intron	N/A	NP_077270.1	Q9H6K1-1
	ILRUN	NM_022758.6		c.314-6955A>T		intron	N/A	NP_073595.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ILRUN	ENST00000374023.8	TSL:1 MANE Select	c.512-6955A>T		intron	N/A	ENSP00000363135.3	Q9H6K1-1
	ILRUN	ENST00000857869.1		c.596-6955A>T		intron	N/A	ENSP00000527928.1
	ILRUN	ENST00000857871.1		c.512-6955A>T		intron	N/A	ENSP00000527930.1

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.2
DANN	Benign	0.86
PhyloP100		-1.5

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: rs2744971; hg19: chr6-34581636;