Variant chr1-78635486-T-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_006820.4(IFI44L):c.873T>A(p.Tyr291Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00645 in 1,610,308 control chromosomes in the GnomAD database, including 38 homozygotes. Variant has been reported in ClinVar as risk factor (no stars). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: 𝑓 0.0047 ( 3 hom., cov: 32)

Exomes 𝑓: 0.0066 ( 35 hom. )

Consequence

IFI44L
NM_006820.4 stop_gained

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -1.51

Variant links:

Genes affected

IFI44L (HGNC:17817): (interferon induced protein 44 like) Predicted to enable GTP binding activity. Involved in defense response to virus. Predicted to be located in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

IFI44L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
IFI44L	NM_006820.4 linkuse as main transcript	c.873T>A	p.Tyr291Ter	stop_gained	5/9	ENST00000370751.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
IFI44L	ENST00000370751.10 linkuse as main transcript	c.873T>A	p.Tyr291Ter	stop_gained	5/9	1	NM_006820.4	P1	Q53G44-1

Frequencies

GnomAD3 genomes

AF:

0.00474

AC:

721

AN:

152114

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00125

Gnomad AMI

AF:

0.00439

Gnomad AMR

AF:

0.00249

Gnomad ASJ

AF:

0.00807

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.00622

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00759

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00532

AC:

1312

AN:

246634

Hom.:

AF XY:

0.00559

AC XY:

744

AN XY:

133158

show subpopulations

Gnomad AFR exome

AF:

0.000988

Gnomad AMR exome

AF:

0.00352

Gnomad ASJ exome

AF:

0.0117

Gnomad EAS exome

AF:

0.000165

Gnomad SAS exome

AF:

0.00220

Gnomad FIN exome

AF:

0.00514

Gnomad NFE exome

AF:

0.00768

Gnomad OTH exome

AF:

0.00365

GnomAD4 exome

AF:

0.00663

AC:

9664

AN:

1458076

Hom.:

Cov.:

AF XY:

0.00650

AC XY:

4712

AN XY:

725198

show subpopulations

Gnomad4 AFR exome

AF:

0.000930

Gnomad4 AMR exome

AF:

0.00340

Gnomad4 ASJ exome

AF:

0.0107

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00213

Gnomad4 FIN exome

AF:

0.00519

Gnomad4 NFE exome

AF:

0.00752

Gnomad4 OTH exome

AF:

0.00582

GnomAD4 genome

AF:

0.00473

AC:

720

AN:

152232

Hom.:

Cov.:

AF XY:

0.00447

AC XY:

333

AN XY:

74430

show subpopulations

Gnomad4 AFR

AF:

0.00125

Gnomad4 AMR

AF:

0.00249

Gnomad4 ASJ

AF:

0.00807

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00145

Gnomad4 FIN

AF:

0.00622

Gnomad4 NFE

AF:

0.00758

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00697

Hom.:

Bravo

AF:

0.00448

TwinsUK

AF:

0.00674

AC:

ALSPAC

AF:

0.00752

AC:

ESP6500AA

AF:

0.000908

AC:

ESP6500EA

AF:

0.00791

AC:

ExAC

AF:

0.00530

AC:

643

Asia WGS

AF:

0.00115

AC:

AN:

3478

EpiCase

AF:

0.00769

EpiControl

AF:

0.00890

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Multisystem inflammatory syndrome in children

Other:1

risk factor, no assertion criteria provided

research

Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital

Nov 14, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Uncertain

0.15

BayesDel_noAF

Pathogenic

0.45

CADD

Pathogenic

DANN

Uncertain

0.99

Eigen

Benign

-0.049

Eigen_PC

Benign

-0.37

FATHMM_MKL

Benign

0.30

MutationTaster

Benign

1.0

A;A

Vest4

0.84

GERP RS

-2.2

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