Genetic Variant IFNW1:c.*310G>C (chr9-21140673-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_002177.3(IFNW1):c.*310G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 173,356 control chromosomes in the GnomAD database, including 8,990 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 0.31 ( 7809 hom., cov: 32)

Exomes 𝑓: 0.33 ( 1181 hom. )

Consequence

IFNW1
NM_002177.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.352

Publications

14 publications found

Variant links:

Genes affected

IFNW1 (HGNC:5448): (interferon omega 1) The protein encoded by this gene is an interferon and possesses antiviral activity. The encoded protein binds to the interferon alpha/beta receptor but not to the interferon gamma receptor. This intronless gene has several pseudogenes spread throughout the genome. [provided by RefSeq, Nov 2015]

IFNW1 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNW1	NM_002177.3 link	c.*310G>C		3_prime_UTR_variant	Exon 1 of 1	ENST00000380229.4	NP_002168.1	P05000A0A7R8GUW6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNW1	ENST00000380229.4 link	c.*310G>C		3_prime_UTR_variant	Exon 1 of 1	6	NM_002177.3	ENSP00000369578.2		P05000

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47496

AN:

151638

Hom.:

7796

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.379

Gnomad AMR

AF:

0.223

Gnomad ASJ

AF:

0.261

Gnomad EAS

AF:

0.162

Gnomad SAS

AF:

0.375

Gnomad FIN

AF:

0.366

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.359

Gnomad OTH

AF:

0.312

GnomAD4 exome

AF:

0.327

AC:

7056

AN:

21600

Hom.:

1181

Cov.:

AF XY:

0.330

AC XY:

3696

AN XY:

11216

show subpopulations

African (AFR)

AF:

0.270

AC:

227

AN:

840

American (AMR)

AF:

0.204

AC:

174

AN:

852

Ashkenazi Jewish (ASJ)

AF:

0.312

AC:

289

AN:

926

East Asian (EAS)

AF:

0.176

AC:

274

AN:

1558

South Asian (SAS)

AF:

0.315

AC:

AN:

292

European-Finnish (FIN)

AF:

0.383

AC:

248

AN:

648

Middle Eastern (MID)

AF:

0.270

AC:

AN:

100

European-Non Finnish (NFE)

AF:

0.352

AC:

5272

AN:

14972

Other (OTH)

AF:

0.321

AC:

453

AN:

1412

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

242

485

727

970

1212

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

102

136

170

<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:

0.313

AC:

47542

AN:

151756

Hom.:

7809

Cov.:

AF XY:

0.313

AC XY:

23248

AN XY:

74166

show subpopulations

African (AFR)

AF:

0.273

AC:

11291

AN:

41372

American (AMR)

AF:

0.223

AC:

3399

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.261

AC:

906

AN:

3472

East Asian (EAS)

AF:

0.161

AC:

833

AN:

5160

South Asian (SAS)

AF:

0.374

AC:

1797

AN:

4802

European-Finnish (FIN)

AF:

0.366

AC:

3838

AN:

10484

Middle Eastern (MID)

AF:

0.274

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.359

AC:

24398

AN:

67888

Other (OTH)

AF:

0.311

AC:

656

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1674

3348

5023

6697

8371

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.319

Hom.:

997

Bravo

AF:

0.296

Asia WGS

AF:

0.285

AC:

986

AN:

3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.83

(source)

DANN

Benign

0.62

PhyloP100

-0.35

Mutation Taster

=100/0

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