Genetic Variant IFRD2:c.-121T>C (chr3-50292395-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006764.5(IFRD2):c.-121T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.698 in 1,586,248 control chromosomes in the GnomAD database, including 391,136 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 0.77 ( 46402 hom., cov: 35)

Exomes 𝑓: 0.69 ( 344734 hom. )

Consequence

IFRD2
NM_006764.5 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.226

Publications

31 publications found

Variant links:

Genes affected

IFRD2 (HGNC:5457): (interferon related developmental regulator 2) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

IFRD2 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=-0.79).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006764.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	IFRD2	NM_006764.5	MANE Select	c.-121T>C		5_prime_UTR	Exon 1 of 12	NP_006755.5

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IFRD2	ENST00000417626.8	TSL:1 MANE Select	c.-121T>C	5_prime_UTR	Exon 1 of 12	ENSP00000402849.4
IFRD2	ENST00000462001.1	TSL:2	n.42T>C	non_coding_transcript_exon	Exon 1 of 2
IFRD2	ENST00000474556.5	TSL:5	n.30T>C	non_coding_transcript_exon	Exon 1 of 11

Frequencies

GnomAD3 genomes

AF:

0.770

AC:

117196

AN:

152126

Hom.:

46340

Cov.:

show subpopulations

Gnomad AFR

AF:

0.946

Gnomad AMI

AF:

0.739

Gnomad AMR

AF:

0.832

Gnomad ASJ

AF:

0.752

Gnomad EAS

AF:

0.770

Gnomad SAS

AF:

0.499

Gnomad FIN

AF:

0.691

Gnomad MID

AF:

0.739

Gnomad NFE

AF:

0.683

Gnomad OTH

AF:

0.769

GnomAD2 exomes

AF:

0.712

AC:

144573

AN:

203022

AF XY:

0.691

show subpopulations

Gnomad AFR exome

AF:

0.949

Gnomad AMR exome

AF:

0.867

Gnomad ASJ exome

AF:

0.755

Gnomad EAS exome

AF:

0.781

Gnomad FIN exome

AF:

0.685

Gnomad NFE exome

AF:

0.683

Gnomad OTH exome

AF:

0.716

GnomAD4 exome

AF:

0.690

AC:

989121

AN:

1434006

Hom.:

344734

Cov.:

AF XY:

0.683

AC XY:

487014

AN XY:

712626

show subpopulations

African (AFR)

AF:

0.954

AC:

31397

AN:

32926

American (AMR)

AF:

0.859

AC:

35975

AN:

41878

Ashkenazi Jewish (ASJ)

AF:

0.753

AC:

19338

AN:

25668

East Asian (EAS)

AF:

0.754

AC:

29038

AN:

38488

South Asian (SAS)

AF:

0.510

AC:

42941

AN:

84158

European-Finnish (FIN)

AF:

0.683

AC:

28149

AN:

41242

Middle Eastern (MID)

AF:

0.696

AC:

3995

AN:

5742

European-Non Finnish (NFE)

AF:

0.684

AC:

755790

AN:

1104268

Other (OTH)

AF:

0.713

AC:

42498

AN:

59636

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.484

Heterozygous variant carriers

19632

39263

58895

78526

98158

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

19432

38864

58296

77728

97160

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.771

AC:

117314

AN:

152242

Hom.:

46402

Cov.:

AF XY:

0.766

AC XY:

57005

AN XY:

74418

show subpopulations

African (AFR)

AF:

0.946

AC:

39317

AN:

41578

American (AMR)

AF:

0.833

AC:

12739

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.752

AC:

2611

AN:

3472

East Asian (EAS)

AF:

0.769

AC:

3968

AN:

5160

South Asian (SAS)

AF:

0.498

AC:

2402

AN:

4828

European-Finnish (FIN)

AF:

0.691

AC:

7322

AN:

10596

Middle Eastern (MID)

AF:

0.736

AC:

215

AN:

292

European-Non Finnish (NFE)

AF:

0.683

AC:

46439

AN:

67996

Other (OTH)

AF:

0.772

AC:

1630

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1357

2713

4070

5426

6783

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

842

1684

2526

3368

4210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.720

Hom.:

43692

Bravo

AF:

0.797

Asia WGS

AF:

0.622

AC:

2166

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

7.9

(source)

DANN

Benign

0.54

PhyloP100

-0.23

PromoterAI

0.097

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over