Variant chr11-320772-A-G details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021034.3(IFITM3):c.42T>C(p.Ser14=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0761 in 1,613,456 control chromosomes in the GnomAD database, including 13,447 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

Frequency

Genomes: 𝑓 0.13 ( 2447 hom., cov: 33)

Exomes 𝑓: 0.070 ( 11000 hom. )

Consequence

IFITM3
NM_021034.3 synonymous

Scores

Clinical Significance

risk factor no assertion criteria provided O:1

Conservation

PhyloP100: -5.37

Variant links:

Genes affected

IFITM3 (HGNC:5414): (interferon induced transmembrane protein 3) Interferon-induced transmembrane (IFITM) proteins are a family of interferon induced antiviral proteins. The family contains five members, including IFITM1, IFITM2 and IFITM3 and belong to the CD225 superfamily. The protein encoded by this gene restricts cellular entry by diverse viral pathogens, such as influenza A virus, Ebola virus and Sars-CoV-2. [provided by RefSeq, Nov 2021]

IFITM3 links:

(HGNC:):

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=-0.88).

BP7

Synonymous conserved (PhyloP=-5.37 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
IFITM3	NM_021034.3 linkuse as main transcript	c.42T>C	p.Ser14=	synonymous_variant	1/2	ENST00000399808.5	NP_066362.2
LOC105376505	XR_007062535.1 linkuse as main transcript	n.287+2026A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
IFITM3	ENST00000399808.5 linkuse as main transcript	c.42T>C	p.Ser14=	synonymous_variant	1/2	1	NM_021034.3	ENSP00000382707	P2
	ENST00000602429.1 linkuse as main transcript	n.94+2026A>G		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.130

AC:

19820

AN:

151944

Hom.:

2447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.250

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.124

Gnomad ASJ

AF:

0.0983

Gnomad EAS

AF:

0.550

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.0780

Gnomad MID

AF:

0.0759

Gnomad NFE

AF:

0.0388

Gnomad OTH

AF:

0.136

GnomAD3 exomes

AF:

0.127

AC:

31738

AN:

249316

Hom.:

4408

AF XY:

0.119

AC XY:

16126

AN XY:

135250

show subpopulations

Gnomad AFR exome

AF:

0.253

Gnomad AMR exome

AF:

0.184

Gnomad ASJ exome

AF:

0.0994

Gnomad EAS exome

AF:

0.560

Gnomad SAS exome

AF:

0.122

Gnomad FIN exome

AF:

0.0782

Gnomad NFE exome

AF:

0.0394

Gnomad OTH exome

AF:

0.0893

GnomAD4 exome

AF:

0.0704

AC:

102914

AN:

1461394

Hom.:

11000

Cov.:

AF XY:

0.0711

AC XY:

51671

AN XY:

727012

show subpopulations

Gnomad4 AFR exome

AF:

0.261

Gnomad4 AMR exome

AF:

0.177

Gnomad4 ASJ exome

AF:

0.0949

Gnomad4 EAS exome

AF:

0.585

Gnomad4 SAS exome

AF:

0.120

Gnomad4 FIN exome

AF:

0.0747

Gnomad4 NFE exome

AF:

0.0358

Gnomad4 OTH exome

AF:

0.0984

GnomAD4 genome

AF:

0.131

AC:

19853

AN:

152062

Hom.:

2447

Cov.:

AF XY:

0.134

AC XY:

9995

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.250

Gnomad4 AMR

AF:

0.124

Gnomad4 ASJ

AF:

0.0983

Gnomad4 EAS

AF:

0.551

Gnomad4 SAS

AF:

0.135

Gnomad4 FIN

AF:

0.0780

Gnomad4 NFE

AF:

0.0388

Gnomad4 OTH

AF:

0.136

Alfa

AF:

0.0744

Hom.:

391

Bravo

AF:

0.146

Asia WGS

AF:

0.299

AC:

1037

AN:

3478

EpiCase

AF:

0.0412

EpiControl

AF:

0.0404

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

Influenza, severe, susceptibility to

Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Jan 06, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

3.1

DANN

Benign

0.53

RBP_binding_hub_radar

1.0

RBP_regulation_power_radar

2.1

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