Genetic Variant IFNA6:c.*239T>A (chr9-21350079-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_021002.2(IFNA6):c.*239T>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 228,022 control chromosomes in the GnomAD database, including 4,071 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 0.18 ( 2611 hom., cov: 32)

Exomes 𝑓: 0.19 ( 1460 hom. )

Consequence

IFNA6
NM_021002.2 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.663

Publications

2 publications found

Variant links:

Genes affected

IFNA6 (HGNC:5427): (interferon alpha 6) 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. Biomarker of anogenital venereal wart. [provided by Alliance of Genome Resources, Apr 2022]

IFNA6 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=-0.8).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA6	NM_021002.2 link	c.*239T>A		downstream_gene_variant		ENST00000380210.2	NP_066282.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNA6	ENST00000380210.2 link	c.*239T>A		downstream_gene_variant		6	NM_021002.2	ENSP00000369558.1
IFNA6	ENST00000259555.5 link	c.*239T>A		downstream_gene_variant		6		ENSP00000259555.5

Frequencies

GnomAD3 genomes

AF:

0.180

AC:

27411

AN:

152102

Hom.:

2609

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.149

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.203

Gnomad EAS

AF:

0.305

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.191

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.167

Gnomad OTH

AF:

0.181

GnomAD4 exome

AF:

0.187

AC:

14171

AN:

75802

Hom.:

1460

Cov.:

AF XY:

0.186

AC XY:

7280

AN XY:

39198

show subpopulations

African (AFR)

AF:

0.184

AC:

365

AN:

1984

American (AMR)

AF:

0.247

AC:

949

AN:

3848

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

505

AN:

2580

East Asian (EAS)

AF:

0.308

AC:

1602

AN:

5194

South Asian (SAS)

AF:

0.119

AC:

331

AN:

2788

European-Finnish (FIN)

AF:

0.197

AC:

1048

AN:

5326

Middle Eastern (MID)

AF:

0.148

AC:

AN:

372

European-Non Finnish (NFE)

AF:

0.172

AC:

8376

AN:

48832

Other (OTH)

AF:

0.193

AC:

940

AN:

4878

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.519

Heterozygous variant carriers

574

1148

1722

2296

2870

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

152

228

304

380

<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:

0.180

AC:

27428

AN:

152220

Hom.:

2611

Cov.:

AF XY:

0.182

AC XY:

13548

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.168

AC:

6980

AN:

41536

American (AMR)

AF:

0.241

AC:

3691

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.203

AC:

703

AN:

3468

East Asian (EAS)

AF:

0.304

AC:

1580

AN:

5190

South Asian (SAS)

AF:

0.110

AC:

528

AN:

4820

European-Finnish (FIN)

AF:

0.191

AC:

2022

AN:

10596

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.167

AC:

11362

AN:

68008

Other (OTH)

AF:

0.181

AC:

383

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1159

2318

3476

4635

5794

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

282

564

846

1128

1410

<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:

0.0986

Hom.:

143

Bravo

AF:

0.186

Asia WGS

AF:

0.189

AC:

656

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

5.0

(source)

DANN

Benign

0.77

PhyloP100

0.66

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