Variant rs1051922 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_002176.4(IFNB1):c.153C>T(p.Tyr51=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 1,613,308 control chromosomes in the GnomAD database, including 92,102 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 0.35 ( 9387 hom., cov: 32)

Exomes 𝑓: 0.33 ( 82715 hom. )

Consequence

IFNB1
NM_002176.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.855

Variant links:

Genes affected

IFNB1 (HGNC:5434): (interferon beta 1) This gene encodes a cytokine that belongs to the interferon family of signaling proteins, which are released as part of the innate immune response to pathogens. The protein encoded by this gene belongs to the type I class of interferons, which are important for defense against viral infections. In addition, type I interferons are involved in cell differentiation and anti-tumor defenses. Following secretion in response to a pathogen, type I interferons bind a homologous receptor complex and induce transcription of genes such as those encoding inflammatory cytokines and chemokines. Overactivation of type I interferon secretion is linked to autoimmune diseases. Mice deficient for this gene display several phenotypes including defects in B cell maturation and increased susceptibility to viral infection. [provided by RefSeq, Sep 2015]

IFNB1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.94).

BP7

Synonymous conserved (PhyloP=-0.855 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFNB1	NM_002176.4 linkuse as main transcript	c.153C>T	p.Tyr51=	synonymous_variant	1/1	ENST00000380232.4	NP_002167.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFNB1	ENST00000380232.4 linkuse as main transcript	c.153C>T	p.Tyr51=	synonymous_variant	1/1		NM_002176.4	ENSP00000369581	P1

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

52985

AN:

151880

Hom.:

9377

Cov.:

show subpopulations

Gnomad AFR

AF:

0.376

Gnomad AMI

AF:

0.210

Gnomad AMR

AF:

0.303

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.338

Gnomad SAS

AF:

0.271

Gnomad FIN

AF:

0.433

Gnomad MID

AF:

0.282

Gnomad NFE

AF:

0.341

Gnomad OTH

AF:

0.304

GnomAD3 exomes

AF:

0.328

AC:

82157

AN:

250568

Hom.:

14045

AF XY:

0.325

AC XY:

44033

AN XY:

135394

show subpopulations

Gnomad AFR exome

AF:

0.376

Gnomad AMR exome

AF:

0.254

Gnomad ASJ exome

AF:

0.314

Gnomad EAS exome

AF:

0.339

Gnomad SAS exome

AF:

0.258

Gnomad FIN exome

AF:

0.433

Gnomad NFE exome

AF:

0.342

Gnomad OTH exome

AF:

0.317

GnomAD4 exome

AF:

0.334

AC:

488312

AN:

1461310

Hom.:

82715

Cov.:

AF XY:

0.332

AC XY:

241664

AN XY:

726978

show subpopulations

Gnomad4 AFR exome

AF:

0.381

Gnomad4 AMR exome

AF:

0.260

Gnomad4 ASJ exome

AF:

0.314

Gnomad4 EAS exome

AF:

0.395

Gnomad4 SAS exome

AF:

0.257

Gnomad4 FIN exome

AF:

0.431

Gnomad4 NFE exome

AF:

0.336

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.349

AC:

53013

AN:

151998

Hom.:

9387

Cov.:

AF XY:

0.353

AC XY:

26186

AN XY:

74280

show subpopulations

Gnomad4 AFR

AF:

0.376

Gnomad4 AMR

AF:

0.303

Gnomad4 ASJ

AF:

0.315

Gnomad4 EAS

AF:

0.338

Gnomad4 SAS

AF:

0.271

Gnomad4 FIN

AF:

0.433

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.304

Alfa

AF:

0.325

Hom.:

13512

Bravo

AF:

0.337

Asia WGS

AF:

0.298

AC:

1039

AN:

3478

EpiCase

AF:

0.332

EpiControl

AF:

0.326

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.28

DANN

Benign

0.17

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over