dbSNP rs2039381: IFNE:p.Gln71* (chr9-21481484-G-A) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_176891.5(IFNE):c.211C>T(p.Gln71*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0218 in 1,614,016 control chromosomes in the GnomAD database, including 2,126 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 0.039 ( 287 hom., cov: 32)

Exomes 𝑓: 0.020 ( 1839 hom. )

Consequence

IFNE
NM_176891.5 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.205

Variant links:

Genes affected

IFNE (HGNC:18163): (interferon epsilon) Predicted to enable cytokine activity and type I interferon receptor binding activity. Predicted to be involved in several processes, including B cell activation; defense response to other organism; and lymphocyte activation involved in immune response. Predicted to be active in extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

IFNE links:

MIR31HG (HGNC:37187): (MIR31 host gene) This gene produces a long non-coding RNA that acts as a host gene for miR-31. This transcript may be involved in cellular pluripotency and regulate the differentiation of myoblasts and other tissues. This RNA was found to interact with Polycomb repressive proteins to repression transcription of genes involves in cell senescence. [provided by RefSeq, Dec 2017]

MIR31HG links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNE	NM_176891.5 link	c.211C>T	p.Gln71*	stop_gained	Exon 1 of 1	ENST00000448696.4	NP_795372.1	Q86WN2A0A7R8GUQ9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNE	ENST00000448696.4 link	c.211C>T	p.Gln71*	stop_gained	Exon 1 of 1	6	NM_176891.5	ENSP00000418018.2		Q86WN2

Frequencies

GnomAD3 genomes

AF:

0.0387

AC:

5894

AN:

152154

Hom.:

287

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0666

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0611

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.155

Gnomad FIN

AF:

0.0185

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00347

Gnomad OTH

AF:

0.0321

GnomAD2 exomes

AF:

0.0454

AC:

11338

AN:

249716

AF XY:

0.0472

show subpopulations

Gnomad AFR exome

AF:

0.0651

Gnomad AMR exome

AF:

0.0504

Gnomad ASJ exome

AF:

0.000597

Gnomad EAS exome

AF:

0.184

Gnomad FIN exome

AF:

0.0184

Gnomad NFE exome

AF:

0.00325

Gnomad OTH exome

AF:

0.0257

GnomAD4 exome

AF:

0.0200

AC:

29258

AN:

1461742

Hom.:

1839

Cov.:

AF XY:

0.0231

AC XY:

16814

AN XY:

727168

show subpopulations

Gnomad4 AFR exome

AF:

0.0731

AC:

2448

AN:

33478

Gnomad4 AMR exome

AF:

0.0516

AC:

2307

AN:

44720

Gnomad4 ASJ exome

AF:

0.000765

AC:

AN:

26136

Gnomad4 EAS exome

AF:

0.182

AC:

7218

AN:

39688

Gnomad4 SAS exome

AF:

0.136

AC:

11770

AN:

86250

Gnomad4 FIN exome

AF:

0.0163

AC:

868

AN:

53402

Gnomad4 NFE exome

AF:

0.00260

AC:

2891

AN:

1111910

Gnomad4 Remaining exome

AF:

0.0278

AC:

1681

AN:

60390

Heterozygous variant carriers

1741

3481

5222

6962

8703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

396

792

1188

1584

1980

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0388

AC:

5901

AN:

152274

Hom.:

287

Cov.:

AF XY:

0.0423

AC XY:

3153

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0666

AC:

0.0666249

AN:

0.0666249

Gnomad4 AMR

AF:

0.0612

AC:

0.0612338

AN:

0.0612338

Gnomad4 ASJ

AF:

0.00115

AC:

0.00115207

AN:

0.00115207

Gnomad4 EAS

AF:

0.182

AC:

0.182169

AN:

0.182169

Gnomad4 SAS

AF:

0.155

AC:

0.154564

AN:

0.154564

Gnomad4 FIN

AF:

0.0185

AC:

0.0184592

AN:

0.0184592

Gnomad4 NFE

AF:

0.00347

AC:

0.00346977

AN:

0.00346977

Gnomad4 OTH

AF:

0.0313

AC:

0.03125

AN:

0.03125

Heterozygous variant carriers

259

519

778

1038

1297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

144

216

288

360

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0160

Hom.:

399

Bravo

AF:

0.0404

TwinsUK

AF:

0.00297

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.0660

AC:

291

ESP6500EA

AF:

0.00279

AC:

ExAC

AF:

0.0449

AC:

5446

Asia WGS

AF:

0.126

AC:

438

AN:

3478

EpiCase

AF:

0.00376

EpiControl

AF:

0.00243

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Pathogenic

0.17

CADD

Pathogenic

DANN

Uncertain

1.0

Eigen

Uncertain

0.34

Eigen_PC

Benign

-0.011

FATHMM_MKL

Benign

0.13

Vest4

0.075

GERP RS

3.8

Mutation Taster

=155/45

polymorphism (auto)

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