Variant 9-21304914-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4BS2

The NM_002169.3(IFNA5):c.343C>T(p.Gln115Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00551 in 1,614,172 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0050 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0056 ( 36 hom. )

Consequence

IFNA5
NM_002169.3 stop_gained

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.75

Variant links:

Genes affected

IFNA5 (HGNC:5426): (interferon alpha 5) 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. [provided by Alliance of Genome Resources, Apr 2022]

IFNA5 links:

LOC107987053 (HGNC:):

LOC107987053 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM4

Stoplost variant in NM_002169.3 Downstream stopcodon found after 208 codons.

BS2

High Homozygotes in GnomAd at 4 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFNA5	NM_002169.3 linkuse as main transcript	c.343C>T	p.Gln115Ter	stop_gained	1/1	ENST00000610521.2
LOC107987053	XR_001746634.2 linkuse as main transcript	n.472-31707G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFNA5	ENST00000610521.2 linkuse as main transcript	c.343C>T	p.Gln115Ter	stop_gained	1/1		NM_002169.3	P1

Frequencies

GnomAD3 genomes

AF:

0.00498

AC:

758

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000748

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00209

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.0198

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00675

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00548

AC:

1379

AN:

251450

Hom.:

AF XY:

0.00514

AC XY:

698

AN XY:

135904

show subpopulations

Gnomad AFR exome

AF:

0.000677

Gnomad AMR exome

AF:

0.00226

Gnomad ASJ exome

AF:

0.00903

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000392

Gnomad FIN exome

AF:

0.0215

Gnomad NFE exome

AF:

0.00608

Gnomad OTH exome

AF:

0.00489

GnomAD4 exome

AF:

0.00557

AC:

8136

AN:

1461892

Hom.:

Cov.:

AF XY:

0.00547

AC XY:

3976

AN XY:

727246

show subpopulations

Gnomad4 AFR exome

AF:

0.000597

Gnomad4 AMR exome

AF:

0.00221

Gnomad4 ASJ exome

AF:

0.00823

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.000591

Gnomad4 FIN exome

AF:

0.0218

Gnomad4 NFE exome

AF:

0.00566

Gnomad4 OTH exome

AF:

0.00464

GnomAD4 genome

AF:

0.00498

AC:

758

AN:

152280

Hom.:

Cov.:

AF XY:

0.00571

AC XY:

425

AN XY:

74456

show subpopulations

Gnomad4 AFR

AF:

0.000746

Gnomad4 AMR

AF:

0.00209

Gnomad4 ASJ

AF:

0.00490

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000623

Gnomad4 FIN

AF:

0.0198

Gnomad4 NFE

AF:

0.00675

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00548

Hom.:

Bravo

AF:

0.00334

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00545

AC:

ESP6500AA

AF:

0.000454

AC:

ESP6500EA

AF:

0.00547

AC:

ExAC

AF:

0.00517

AC:

628

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00529

EpiControl

AF:

0.00439

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

Aug 23, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.14

BayesDel_noAF

Uncertain

0.040

Cadd

Pathogenic

Dann

Uncertain

0.98

Eigen

Benign

0.064

Eigen_PC

Benign

-0.30

FATHMM_MKL

Benign

0.066

MutationTaster

Benign

1.0

Vest4

0.042

GERP RS

2.3

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

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