Variant rs9298814 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021268.2(IFNA17):c.551T>G(p.Ile184Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.206 in 1,473,920 control chromosomes in the GnomAD database, including 47,321 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.28 ( 6531 hom., cov: 32)

Exomes 𝑓: 0.20 ( 40790 hom. )

Consequence

IFNA17
NM_021268.2 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.760

Variant links:

Genes affected

IFNA17 (HGNC:5422): (interferon alpha 17) Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including B cell activation; lymphocyte activation involved in immune response; and positive regulation of peptidyl-serine phosphorylation of STAT protein. Predicted to be located in extracellular region. Predicted to be active in extracellular space. Implicated in Crimean-Congo hemorrhagic fever and sarcoidosis. [provided by Alliance of Genome Resources, Apr 2022]

IFNA17 links:

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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 (MetaRNN=0.011078656).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.502 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNA17	NM_021268.2 linkuse as main transcript	c.551T>G	p.Ile184Arg	missense_variant	1/1	ENST00000413767.2	NP_067091.1	P01571A0A7R8C355

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNA17	ENST00000413767.2 linkuse as main transcript	c.551T>G	p.Ile184Arg	missense_variant	1/1	6	NM_021268.2	ENSP00000411940.2		P01571

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42376

AN:

151646

Hom.:

6522

Cov.:

show subpopulations

Gnomad AFR

AF:

0.377

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.518

Gnomad SAS

AF:

0.193

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.237

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.269

GnomAD3 exomes

AF:

0.116

AC:

26310

AN:

226892

Hom.:

5071

AF XY:

0.103

AC XY:

12728

AN XY:

123150

show subpopulations

Gnomad AFR exome

AF:

0.212

Gnomad AMR exome

AF:

0.151

Gnomad ASJ exome

AF:

0.0652

Gnomad EAS exome

AF:

0.354

Gnomad SAS exome

AF:

0.0569

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.0772

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.198

AC:

261478

AN:

1322160

Hom.:

40790

Cov.:

AF XY:

0.196

AC XY:

129582

AN XY:

660462

show subpopulations

Gnomad4 AFR exome

AF:

0.350

Gnomad4 AMR exome

AF:

0.312

Gnomad4 ASJ exome

AF:

0.213

Gnomad4 EAS exome

AF:

0.548

Gnomad4 SAS exome

AF:

0.167

Gnomad4 FIN exome

AF:

0.197

Gnomad4 NFE exome

AF:

0.177

Gnomad4 OTH exome

AF:

0.215

GnomAD4 genome

AF:

0.280

AC:

42426

AN:

151760

Hom.:

6531

Cov.:

AF XY:

0.279

AC XY:

20687

AN XY:

74136

show subpopulations

Gnomad4 AFR

AF:

0.377

Gnomad4 AMR

AF:

0.311

Gnomad4 ASJ

AF:

0.241

Gnomad4 EAS

AF:

0.518

Gnomad4 SAS

AF:

0.195

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.111

Hom.:

333

Bravo

AF:

0.295

ESP6500AA

AF:

0.130

AC:

572

ESP6500EA

AF:

0.0527

AC:

453

ExAC

AF:

0.0812

AC:

9844

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.042

BayesDel_addAF

Benign

-0.80

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.82

DANN

Benign

0.54

DEOGEN2

Benign

0.025

Eigen

Benign

-1.8

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.000070

LIST_S2

Benign

0.066

MetaRNN

Benign

0.011

MetaSVM

Benign

-0.95

MutationAssessor

Benign

-3.5

PrimateAI

Benign

0.44

PROVEAN

Benign

5.5

REVEL

Benign

0.041

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.044

MPC

0.015

ClinPred

0.0079

GERP RS

0.95

Varity_R

0.037

gMVP

0.033

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

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