dbSNP rs1583005: IK:c.177-136G>A (chr5-140651952-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006083.4(IK):c.177-136G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.424 in 820,686 control chromosomes in the GnomAD database, including 75,134 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 0.41 ( 13274 hom., cov: 32)

Exomes 𝑓: 0.43 ( 61860 hom. )

Consequence

IK
NM_006083.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0430

Publications

28 publications found

Variant links:

Genes affected

IK (HGNC:5958): (IK cytokine) The protein encoded by this gene was identified by its RED repeat, a stretch of repeated arginine, glutamic acid and aspartic acid residues. The protein localizes to discrete dots within the nucleus, excluding the nucleolus. Its function is unknown. This gene maps to chromosome 5; however, a pseudogene may exist on chromosome 2. [provided by RefSeq, Jul 2008]

IK 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006083.4. 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
	IK	NM_006083.4	MANE Select	c.177-136G>A		intron	N/A	NP_006074.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
IK	ENST00000417647.7	TSL:1 MANE Select	c.177-136G>A	intron	N/A	ENSP00000396301.2
IK	ENST00000508301.5	TSL:2	c.177-136G>A	intron	N/A	ENSP00000422641.1
IK	ENST00000502899.2	TSL:3	c.177-136G>A	intron	N/A	ENSP00000426764.2

Frequencies

GnomAD3 genomes

AF:

0.414

AC:

62906

AN:

151824

Hom.:

13254

Cov.:

show subpopulations

Gnomad AFR

AF:

0.372

Gnomad AMI

AF:

0.177

Gnomad AMR

AF:

0.402

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.460

Gnomad SAS

AF:

0.430

Gnomad FIN

AF:

0.532

Gnomad MID

AF:

0.291

Gnomad NFE

AF:

0.424

Gnomad OTH

AF:

0.396

GnomAD4 exome

AF:

0.427

AC:

285417

AN:

668742

Hom.:

61860

Cov.:

AF XY:

0.425

AC XY:

150904

AN XY:

354936

show subpopulations

African (AFR)

AF:

0.369

AC:

6294

AN:

17050

American (AMR)

AF:

0.386

AC:

12115

AN:

31410

Ashkenazi Jewish (ASJ)

AF:

0.421

AC:

7949

AN:

18874

East Asian (EAS)

AF:

0.467

AC:

16326

AN:

34934

South Asian (SAS)

AF:

0.408

AC:

25724

AN:

63048

European-Finnish (FIN)

AF:

0.531

AC:

26957

AN:

50734

Middle Eastern (MID)

AF:

0.355

AC:

1468

AN:

4134

European-Non Finnish (NFE)

AF:

0.420

AC:

174290

AN:

414632

Other (OTH)

AF:

0.421

AC:

14294

AN:

33926

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

8285

16570

24855

33140

41425

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2398

4796

7194

9592

11990

<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:

0.414

AC:

62963

AN:

151944

Hom.:

13274

Cov.:

AF XY:

0.420

AC XY:

31174

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.372

AC:

15396

AN:

41434

American (AMR)

AF:

0.402

AC:

6134

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.431

AC:

1494

AN:

3468

East Asian (EAS)

AF:

0.460

AC:

2377

AN:

5168

South Asian (SAS)

AF:

0.430

AC:

2071

AN:

4816

European-Finnish (FIN)

AF:

0.532

AC:

5596

AN:

10528

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.424

AC:

28800

AN:

67950

Other (OTH)

AF:

0.401

AC:

847

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1888

3775

5663

7550

9438

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

600

1200

1800

2400

3000

<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:

0.419

Hom.:

26577

Bravo

AF:

0.399

Asia WGS

AF:

0.518

AC:

1798

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

1.6

(source)

DANN

Benign

0.27

PhyloP100

-0.043

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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