Variant chr9-21207006-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002171.2(IFNA10):c.92G>C(p.Ser31Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 1,565,108 control chromosomes in the GnomAD database, including 48,087 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.28 ( 6545 hom., cov: 31)

Exomes 𝑓: 0.22 ( 41542 hom. )

Consequence

IFNA10
NM_002171.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.20

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=8.291304E-4).

BP6

Variant 9-21207006-C-G is Benign according to our data. Variant chr9-21207006-C-G is described in ClinVar as [Benign]. Clinvar id is 768284.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFNA10	NM_002171.2 linkuse as main transcript	c.92G>C	p.Ser31Thr	missense_variant	1/1	ENST00000357374.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNA10	ENST00000357374.2 linkuse as main transcript	c.92G>C	p.Ser31Thr	missense_variant	1/1		NM_002171.2	P1

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42146

AN:

151020

Hom.:

6536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.377

Gnomad AMI

AF:

0.168

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.511

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.214

Gnomad MID

AF:

0.234

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.269

GnomAD3 exomes

AF:

0.235

AC:

55190

AN:

234830

Hom.:

9104

AF XY:

0.221

AC XY:

28038

AN XY:

127058

show subpopulations

Gnomad AFR exome

AF:

0.348

Gnomad AMR exome

AF:

0.335

Gnomad ASJ exome

AF:

0.182

Gnomad EAS exome

AF:

0.517

Gnomad SAS exome

AF:

0.166

Gnomad FIN exome

AF:

0.193

Gnomad NFE exome

AF:

0.174

Gnomad OTH exome

AF:

0.211

GnomAD4 exome

AF:

0.219

AC:

310158

AN:

1413966

Hom.:

41542

Cov.:

AF XY:

0.217

AC XY:

153208

AN XY:

704936

show subpopulations

Gnomad4 AFR exome

AF:

0.367

Gnomad4 AMR exome

AF:

0.352

Gnomad4 ASJ exome

AF:

0.225

Gnomad4 EAS exome

AF:

0.541

Gnomad4 SAS exome

AF:

0.184

Gnomad4 FIN exome

AF:

0.207

Gnomad4 NFE exome

AF:

0.200

Gnomad4 OTH exome

AF:

0.231

GnomAD4 genome

AF:

0.279

AC:

42201

AN:

151142

Hom.:

6545

Cov.:

AF XY:

0.278

AC XY:

20564

AN XY:

73842

show subpopulations

Gnomad4 AFR

AF:

0.377

Gnomad4 AMR

AF:

0.310

Gnomad4 ASJ

AF:

0.239

Gnomad4 EAS

AF:

0.511

Gnomad4 SAS

AF:

0.200

Gnomad4 FIN

AF:

0.214

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.268

Alfa

AF:

0.223

Hom.:

1355

Bravo

AF:

0.296

ExAC

AF:

0.236

AC:

28681

Asia WGS

AF:

0.337

AC:

1170

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.092

BayesDel_addAF

Benign

-0.78

BayesDel_noAF

Benign

-0.75

CADD

Benign

0.52

DANN

Benign

0.77

DEOGEN2

Benign

0.0020

Eigen

Benign

-0.91

Eigen_PC

Benign

-1.1

FATHMM_MKL

Benign

0.018

LIST_S2

Benign

0.10

MetaRNN

Benign

0.00083

MetaSVM

Benign

-0.98

MutationAssessor

Uncertain

2.1

MutationTaster

Benign

1.0

PrimateAI

Benign

0.26

PROVEAN

Benign

-1.4

REVEL

Benign

0.031

Sift

Benign

0.089

Sift4G

Benign

0.39

Polyphen

0.095

Vest4

0.050

MPC

0.17

ClinPred

0.0092

GERP RS

-1.1

Varity_R

0.16

gMVP

0.16

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over