Genetic Variant NM_002171.2:c.60T>A (chr9-21207038-A-T) – ACMG Classification: Benign (-8 pts)

Variant summary

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

The NM_002171.2(IFNA10):c.60T>A(p.Cys20*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 1,508,488 control chromosomes in the GnomAD database, including 47,160 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 0.28 ( 6515 hom., cov: 31)

Exomes 𝑓: 0.21 ( 40645 hom. )

Consequence

IFNA10
NM_002171.2 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.638

Publications

28 publications found

Variant links:

Genes affected

IFNA10 (HGNC:5418): (interferon alpha 10) This gene encodes a protein that belongs to the type I interferon family of proteins, and is located in a cluster of alpha interferon genes on chromosome 9. Interferons are small regulatory molecules that function in cell signaling in response to viruses and other pathogens or tumor cells. This gene is intronless and the encoded protein is secreted. [provided by RefSeq, Aug 2013]

IFNA10 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 = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFNA10	NM_002171.2 link	c.60T>A	p.Cys20*	stop_gained	Exon 1 of 1	ENST00000357374.2	NP_002162.1	P01566A0A7R8C2Z1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFNA10	ENST00000357374.2 link	c.60T>A	p.Cys20*	stop_gained	Exon 1 of 1	6	NM_002171.2	ENSP00000369566.1		P01566

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42027

AN:

150904

Hom.:

6506

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.241

Gnomad EAS

AF:

0.508

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.269

GnomAD2 exomes

AF:

0.216

AC:

49259

AN:

227702

AF XY:

0.203

show subpopulations

Gnomad AFR exome

AF:

0.330

Gnomad AMR exome

AF:

0.304

Gnomad ASJ exome

AF:

0.160

Gnomad EAS exome

AF:

0.507

Gnomad FIN exome

AF:

0.183

Gnomad NFE exome

AF:

0.157

Gnomad OTH exome

AF:

0.194

GnomAD4 exome

AF:

0.206

AC:

279840

AN:

1357462

Hom.:

40645

Cov.:

AF XY:

0.204

AC XY:

138193

AN XY:

676962

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.356

AC:

10709

AN:

30068

American (AMR)

AF:

0.334

AC:

13985

AN:

41854

Ashkenazi Jewish (ASJ)

AF:

0.211

AC:

5227

AN:

24720

East Asian (EAS)

AF:

0.541

AC:

20971

AN:

38766

South Asian (SAS)

AF:

0.176

AC:

14743

AN:

83578

European-Finnish (FIN)

AF:

0.205

AC:

10827

AN:

52914

Middle Eastern (MID)

AF:

0.195

AC:

1072

AN:

5494

European-Non Finnish (NFE)

AF:

0.186

AC:

189879

AN:

1023496

Other (OTH)

AF:

0.220

AC:

12427

AN:

56572

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.332

Heterozygous variant carriers

10818

21636

32455

43273

54091

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

6264

12528

18792

25056

31320

<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:

0.279

AC:

42081

AN:

151026

Hom.:

6515

Cov.:

AF XY:

0.278

AC XY:

20495

AN XY:

73774

show subpopulations

African (AFR)

AF:

0.376

AC:

15355

AN:

40864

American (AMR)

AF:

0.309

AC:

4696

AN:

15186

Ashkenazi Jewish (ASJ)

AF:

0.241

AC:

834

AN:

3466

East Asian (EAS)

AF:

0.507

AC:

2575

AN:

5074

South Asian (SAS)

AF:

0.201

AC:

966

AN:

4814

European-Finnish (FIN)

AF:

0.213

AC:

2251

AN:

10552

Middle Eastern (MID)

AF:

0.240

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.216

AC:

14615

AN:

67760

Other (OTH)

AF:

0.268

AC:

565

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

1300

2600

3899

5199

6499

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

410

820

1230

1640

2050

<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:

0.168

Hom.:

715

Bravo

AF:

0.296

ExAC

AF:

0.225

AC:

27227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.30

BayesDel_noAF

Uncertain

-0.060

CADD

Pathogenic

(source)

DANN

Uncertain

0.99

Eigen

Benign

-0.33

Eigen_PC

Benign

-0.71

FATHMM_MKL

Benign

0.0023

PhyloP100

-0.64

Vest4

0.023

GERP RS

-0.94

PromoterAI

0.012

Neutral

(source)

Mutation Taster

=187/13

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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