Variant rs11554159 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_006332.5(IFI30):c.227G>A(p.Arg76Gln) variant causes a missense change. The variant allele was found at a frequency of 0.255 in 1,611,462 control chromosomes in the GnomAD database, including 53,986 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 0.24 ( 4531 hom., cov: 32)

Exomes 𝑓: 0.26 ( 49455 hom. )

Consequence

IFI30
NM_006332.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.77

Variant links:

Genes affected

IFI30 (HGNC:5398): (IFI30 lysosomal thiol reductase) The protein encoded by this gene is a lysosomal thiol reductase that at low pH can reduce protein disulfide bonds. The enzyme is expressed constitutively in antigen-presenting cells and induced by gamma-interferon in other cell types. This enzyme has an important role in MHC class II-restricted antigen processing. [provided by RefSeq, Jul 2008]

IFI30 links:

ENSG00000268173 (HGNC:):

ENSG00000268173 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017537773).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFI30	NM_006332.5 linkuse as main transcript	c.227G>A	p.Arg76Gln	missense_variant	2/7	ENST00000407280.4	NP_006323.2	P13284A0A024R7N7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
IFI30	ENST00000407280.4 linkuse as main transcript	c.227G>A	p.Arg76Gln	missense_variant	2/7	1	NM_006332.5	ENSP00000384886.1	P13284
ENSG00000268173	ENST00000593731.1 linkuse as main transcript	n.*1663G>A		non_coding_transcript_exon_variant	20/25	2		ENSP00000471914.1
ENSG00000268173	ENST00000593731.1 linkuse as main transcript	n.*1663G>A		3_prime_UTR_variant	20/25	2		ENSP00000471914.1

Frequencies

GnomAD3 genomes

AF:

0.242

AC:

36820

AN:

151942

Hom.:

4528

Cov.:

show subpopulations

Gnomad AFR

AF:

0.236

Gnomad AMI

AF:

0.194

Gnomad AMR

AF:

0.202

Gnomad ASJ

AF:

0.316

Gnomad EAS

AF:

0.0700

Gnomad SAS

AF:

0.170

Gnomad FIN

AF:

0.256

Gnomad MID

AF:

0.294

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.265

GnomAD3 exomes

AF:

0.228

AC:

55720

AN:

244546

Hom.:

6860

AF XY:

0.232

AC XY:

30885

AN XY:

132846

show subpopulations

Gnomad AFR exome

AF:

0.236

Gnomad AMR exome

AF:

0.169

Gnomad ASJ exome

AF:

0.336

Gnomad EAS exome

AF:

0.0773

Gnomad SAS exome

AF:

0.190

Gnomad FIN exome

AF:

0.258

Gnomad NFE exome

AF:

0.262

Gnomad OTH exome

AF:

0.255

GnomAD4 exome

AF:

0.256

AC:

373997

AN:

1459402

Hom.:

49455

Cov.:

AF XY:

0.256

AC XY:

185515

AN XY:

725784

show subpopulations

Gnomad4 AFR exome

AF:

0.237

Gnomad4 AMR exome

AF:

0.173

Gnomad4 ASJ exome

AF:

0.328

Gnomad4 EAS exome

AF:

0.0798

Gnomad4 SAS exome

AF:

0.191

Gnomad4 FIN exome

AF:

0.253

Gnomad4 NFE exome

AF:

0.270

Gnomad4 OTH exome

AF:

0.255

GnomAD4 genome

AF:

0.242

AC:

36837

AN:

152060

Hom.:

4531

Cov.:

AF XY:

0.240

AC XY:

17823

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.236

Gnomad4 AMR

AF:

0.201

Gnomad4 ASJ

AF:

0.316

Gnomad4 EAS

AF:

0.0701

Gnomad4 SAS

AF:

0.171

Gnomad4 FIN

AF:

0.256

Gnomad4 NFE

AF:

0.267

Gnomad4 OTH

AF:

0.261

Alfa

AF:

0.254

Hom.:

6629

Bravo

AF:

0.243

TwinsUK

AF:

0.267

AC:

990

ALSPAC

AF:

0.279

AC:

1076

ESP6500AA

AF:

0.219

AC:

905

ESP6500EA

AF:

0.256

AC:

2157

ExAC

AF:

0.224

AC:

27090

Asia WGS

AF:

0.117

AC:

410

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.27

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.095

T;T

Eigen

Benign

0.053

Eigen_PC

Benign

-0.014

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.84

T;D

MetaRNN

Benign

0.0018

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.7

.;L

PrimateAI

Uncertain

0.52

PROVEAN

Uncertain

-3.8

.;D

REVEL

Uncertain

0.36

Sift

Benign

0.083

.;T

Sift4G

Uncertain

0.028

D;T

Polyphen

1.0

.;D

Vest4

0.14

MPC

0.087

ClinPred

0.032

GERP RS

4.2

Varity_R

0.28

gMVP

0.65

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over