Genetic Variant NM_002177.3: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:

Genome browser will be placed here

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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