dbSNP rs1333973: IFI44L:n.2727T>A (chr1-78628396-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000486882.5(IFI44L):n.2727T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 1,482,864 control chromosomes in the GnomAD database, including 95,164 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 ( 9790 hom., cov: 32)

Exomes 𝑓: 0.35 ( 85374 hom. )

Consequence

IFI44L
ENST00000486882.5 non_coding_transcript_exon

Scores

Splicing: ADA: 0.00001621

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.684

Publications

28 publications found

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 was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.69).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFI44L	NM_006820.4 link	c.478+3T>A		splice_region_variant, intron_variant	Intron 2 of 8	ENST00000370751.10	NP_006811.2	Q53G44-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFI44L	ENST00000370751.10 link	c.478+3T>A		splice_region_variant, intron_variant	Intron 2 of 8	1	NM_006820.4	ENSP00000359787.4		Q53G44-1
IFI44L	ENST00000459784.6 link	c.-296-555T>A		intron_variant	Intron 2 of 8	3		ENSP00000506096.1		B4E019

Frequencies

GnomAD3 genomes

AF:

0.347

AC:

52724

AN:

151816

Hom.:

9781

Cov.:

show subpopulations

Gnomad AFR

AF:

0.309

Gnomad AMI

AF:

0.247

Gnomad AMR

AF:

0.331

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.761

Gnomad SAS

AF:

0.426

Gnomad FIN

AF:

0.395

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.331

Gnomad OTH

AF:

0.371

GnomAD2 exomes

AF:

0.381

AC:

77914

AN:

204398

AF XY:

0.381

show subpopulations

Gnomad AFR exome

AF:

0.306

Gnomad AMR exome

AF:

0.362

Gnomad ASJ exome

AF:

0.330

Gnomad EAS exome

AF:

0.756

Gnomad FIN exome

AF:

0.398

Gnomad NFE exome

AF:

0.327

Gnomad OTH exome

AF:

0.373

GnomAD4 exome

AF:

0.348

AC:

462716

AN:

1330932

Hom.:

85374

Cov.:

AF XY:

0.349

AC XY:

231604

AN XY:

663152

show subpopulations

African (AFR)

AF:

0.305

AC:

8863

AN:

29026

American (AMR)

AF:

0.354

AC:

11697

AN:

33026

Ashkenazi Jewish (ASJ)

AF:

0.323

AC:

7289

AN:

22560

East Asian (EAS)

AF:

0.784

AC:

30428

AN:

38794

South Asian (SAS)

AF:

0.417

AC:

31111

AN:

74648

European-Finnish (FIN)

AF:

0.388

AC:

19710

AN:

50744

Middle Eastern (MID)

AF:

0.372

AC:

1551

AN:

4174

European-Non Finnish (NFE)

AF:

0.324

AC:

331568

AN:

1022660

Other (OTH)

AF:

0.371

AC:

20499

AN:

55300

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.497

Heterozygous variant carriers

14177

28355

42532

56710

70887

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.347

AC:

52778

AN:

151932

Hom.:

9790

Cov.:

AF XY:

0.354

AC XY:

26252

AN XY:

74254

show subpopulations

African (AFR)

AF:

0.310

AC:

12830

AN:

41448

American (AMR)

AF:

0.331

AC:

5059

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

1124

AN:

3468

East Asian (EAS)

AF:

0.761

AC:

3928

AN:

5164

South Asian (SAS)

AF:

0.425

AC:

2052

AN:

4824

European-Finnish (FIN)

AF:

0.395

AC:

4162

AN:

10526

Middle Eastern (MID)

AF:

0.348

AC:

101

AN:

290

European-Non Finnish (NFE)

AF:

0.331

AC:

22510

AN:

67924

Other (OTH)

AF:

0.374

AC:

787

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1695

3390

5086

6781

8476

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.335

Hom.:

1688

Bravo

AF:

0.341

Asia WGS

AF:

0.561

AC:

1948

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.69

CADD

Benign

(source)

DANN

Benign

0.53

PhyloP100

0.68

PromoterAI

0.052

Neutral

(source)

Mutation Taster

=86/14

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000016

dbscSNV1_RF

Benign

0.0060

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

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rs1333973

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over