6-34651116-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024294.4(ILRUN):​c.313+3509C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 152,000 control chromosomes in the GnomAD database, including 2,276 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 ( 2276 hom., cov: 31)

Consequence

ILRUN
NM_024294.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.630
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ILRUNNM_024294.4 linkuse as main transcriptc.313+3509C>T intron_variant ENST00000374023.8 NP_077270.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ILRUNENST00000374023.8 linkuse as main transcriptc.313+3509C>T intron_variant 1 NM_024294.4 ENSP00000363135 P1Q9H6K1-1
ILRUNENST00000374021.1 linkuse as main transcriptc.91+3509C>T intron_variant 3 ENSP00000363133
ILRUNENST00000374026.7 linkuse as main transcriptc.313+3509C>T intron_variant 2 ENSP00000363138 Q9H6K1-2

Frequencies

GnomAD3 genomes
AF:
0.165
AC:
25122
AN:
151882
Hom.:
2273
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.225
Gnomad AMI
AF:
0.169
Gnomad AMR
AF:
0.123
Gnomad ASJ
AF:
0.168
Gnomad EAS
AF:
0.0114
Gnomad SAS
AF:
0.0813
Gnomad FIN
AF:
0.216
Gnomad MID
AF:
0.158
Gnomad NFE
AF:
0.149
Gnomad OTH
AF:
0.157
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.165
AC:
25143
AN:
152000
Hom.:
2276
Cov.:
31
AF XY:
0.166
AC XY:
12364
AN XY:
74274
show subpopulations
Gnomad4 AFR
AF:
0.225
Gnomad4 AMR
AF:
0.123
Gnomad4 ASJ
AF:
0.168
Gnomad4 EAS
AF:
0.0114
Gnomad4 SAS
AF:
0.0801
Gnomad4 FIN
AF:
0.216
Gnomad4 NFE
AF:
0.149
Gnomad4 OTH
AF:
0.156
Alfa
AF:
0.144
Hom.:
3656
Bravo
AF:
0.162
Asia WGS
AF:
0.0470
AC:
164
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
1.9
DANN
Benign
0.45

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2814993; hg19: chr6-34618893; API