Genetic Variant NM_006764.5: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IFRD2	NM_006764.5 link	c.-121T>C		5_prime_UTR_variant	Exon 1 of 12	ENST00000417626.8	NP_006755.5	Q12894

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
IFRD2	ENST00000417626.8 link	c.-121T>C		5_prime_UTR_variant	Exon 1 of 12	1	NM_006764.5	ENSP00000402849.4		Q12894

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over