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

Publications

27 publications found

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

African (AFR)

AF:

0.0731

AC:

2448

AN:

33478

American (AMR)

AF:

0.0516

AC:

2307

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.000765

AC:

AN:

26136

East Asian (EAS)

AF:

0.182

AC:

7218

AN:

39688

South Asian (SAS)

AF:

0.136

AC:

11770

AN:

86250

European-Finnish (FIN)

AF:

0.0163

AC:

868

AN:

53402

Middle Eastern (MID)

AF:

0.00954

AC:

AN:

5768

European-Non Finnish (NFE)

AF:

0.00260

AC:

2891

AN:

1111910

Other (OTH)

AF:

0.0278

AC:

1681

AN:

60390

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.471

Heterozygous variant carriers

1741

3481

5222

6962

8703

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

African (AFR)

AF:

0.0666

AC:

2768

AN:

41546

American (AMR)

AF:

0.0612

AC:

937

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.00115

AC:

AN:

3472

East Asian (EAS)

AF:

0.182

AC:

944

AN:

5182

South Asian (SAS)

AF:

0.155

AC:

745

AN:

4820

European-Finnish (FIN)

AF:

0.0185

AC:

196

AN:

10618

Middle Eastern (MID)

AF:

0.0170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00347

AC:

236

AN:

68016

Other (OTH)

AF:

0.0313

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

259

519

778

1038

1297

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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

(source)

DANN

Uncertain

1.0

Eigen

Uncertain

0.34

Eigen_PC

Benign

-0.011

FATHMM_MKL

Benign

0.13

PhyloP100

0.20

Vest4

0.075

GERP RS

3.8

Mutation Taster

=155/45

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over