Variant 9-21207001-C-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_002171.2(IFNA10):c.97G>C(p.Gly33Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 1,585,982 control chromosomes in the GnomAD database, including 48,179 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6533 hom., cov: 31)

Exomes 𝑓: 0.22 ( 41646 hom. )

Consequence

IFNA10
NM_002171.2 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -2.14

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0019498467).

BP6

Variant 9-21207001-C-G is Benign according to our data. Variant chr9-21207001-C-G is described in ClinVar as [Benign]. Clinvar id is 768283.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.494 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.97G>C	p.Gly33Arg	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.97G>C	p.Gly33Arg	missense_variant	1/1		NM_002171.2	P1

Frequencies

GnomAD3 genomes

AF:

0.279

AC:

42125

AN:

151026

Hom.:

6524

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.169

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.240

Gnomad EAS

AF:

0.510

Gnomad SAS

AF:

0.198

Gnomad FIN

AF:

0.213

Gnomad MID

AF:

0.239

Gnomad NFE

AF:

0.216

Gnomad OTH

AF:

0.268

GnomAD3 exomes

AF:

0.237

AC:

55705

AN:

235466

Hom.:

9189

AF XY:

0.222

AC XY:

28271

AN XY:

127242

show subpopulations

Gnomad AFR exome

AF:

0.350

Gnomad AMR exome

AF:

0.337

Gnomad ASJ exome

AF:

0.184

Gnomad EAS exome

AF:

0.518

Gnomad SAS exome

AF:

0.167

Gnomad FIN exome

AF:

0.194

Gnomad NFE exome

AF:

0.177

Gnomad OTH exome

AF:

0.212

GnomAD4 exome

AF:

0.224

AC:

320795

AN:

1434832

Hom.:

41646

Cov.:

AF XY:

0.221

AC XY:

158210

AN XY:

714700

show subpopulations

Gnomad4 AFR exome

AF:

0.368

Gnomad4 AMR exome

AF:

0.352

Gnomad4 ASJ exome

AF:

0.227

Gnomad4 EAS exome

AF:

0.541

Gnomad4 SAS exome

AF:

0.185

Gnomad4 FIN exome

AF:

0.207

Gnomad4 NFE exome

AF:

0.206

Gnomad4 OTH exome

AF:

0.235

GnomAD4 genome

AF:

0.279

AC:

42180

AN:

151150

Hom.:

6533

Cov.:

AF XY:

0.278

AC XY:

20542

AN XY:

73848

show subpopulations

Gnomad4 AFR

AF:

0.376

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.240

Gnomad4 EAS

AF:

0.510

Gnomad4 SAS

AF:

0.200

Gnomad4 FIN

AF:

0.213

Gnomad4 NFE

AF:

0.216

Gnomad4 OTH

AF:

0.267

Alfa

AF:

0.177

Hom.:

879

Bravo

AF:

0.296

ExAC

AF:

0.236

AC:

28693

Asia WGS

AF:

0.337

AC:

1172

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.83

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.011

DANN

Benign

0.60

DEOGEN2

Benign

0.00064

Eigen

Benign

-1.4

Eigen_PC

Benign

-1.5

FATHMM_MKL

Benign

0.0096

LIST_S2

Benign

0.12

MetaRNN

Benign

0.0019

MetaSVM

Benign

-0.92

MutationAssessor

Benign

1.0

MutationTaster

Benign

1.0

PrimateAI

Benign

0.26

PROVEAN

Benign

-0.97

REVEL

Benign

0.013

Sift

Benign

0.78

Sift4G

Benign

0.54

Polyphen

0.017

Vest4

0.018

MPC

0.13

ClinPred

0.0034

GERP RS

-4.7

Varity_R

0.077

gMVP

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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