Genetic Variant CSNK2A2IP:p.Ile197Ile (chr3-88465948-C-T) – ACMG Classification: Benign (-7 pts)

Variant summary

Our verdict is Benign. The variant received -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001368165.1(CSNK2A2IP):c.591C>T(p.Ile197Ile) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000637 in 1,231,620 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00089 ( 0 hom., cov: 32)

Exomes 𝑓: 0.00060 ( 1 hom. )

Consequence

CSNK2A2IP
NM_001368165.1 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.527

Publications

0 publications found

Variant links:

Genes affected

CSNK2A2IP (HGNC:53637): (casein kinase 2 subunit alpha' interacting protein) Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

CSNK2A2IP links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -7 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BP6

Variant 3-88465948-C-T is Benign according to our data. Variant chr3-88465948-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 2653988.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=-0.527 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001368165.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
CSNK2A2IP	NM_001368165.1	MANE Select	c.591C>T	p.Ile197Ile	synonymous	Exon 2 of 2	NP_001355094.1	A0A1B0GTH6
CSNK2A2IP	NM_001368166.1		c.591C>T	p.Ile197Ile	synonymous	Exon 3 of 3	NP_001355095.1	A0A1B0GTH6
CSNK2A2IP	NM_001368167.1		c.591C>T	p.Ile197Ile	synonymous	Exon 3 of 3	NP_001355096.1	A0A1B0GTH6

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK2A2IP	ENST00000637986.2	TSL:4 MANE Select	c.591C>T	p.Ile197Ile	synonymous	Exon 2 of 2	ENSP00000489704.1	A0A1B0GTH6

Frequencies

GnomAD3 genomes

AF:

0.000881

AC:

134

AN:

152146

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000121

Gnomad AMI

AF:

0.0241

Gnomad AMR

AF:

0.000721

Gnomad ASJ

AF:

0.000288

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00269

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00109

Gnomad OTH

AF:

0.00383

GnomAD4 exome

AF:

0.000601

AC:

649

AN:

1079356

Hom.:

Cov.:

AF XY:

0.000605

AC XY:

308

AN XY:

509488

show subpopulations

African (AFR)

AF:

0.0000435

AC:

AN:

22966

American (AMR)

AF:

0.000594

AC:

AN:

8416

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14390

East Asian (EAS)

AF:

0.0000754

AC:

AN:

26524

South Asian (SAS)

AF:

0.00287

AC:

AN:

19492

European-Finnish (FIN)

AF:

0.000190

AC:

AN:

21102

Middle Eastern (MID)

AF:

0.00343

AC:

AN:

2916

European-Non Finnish (NFE)

AF:

0.000591

AC:

544

AN:

919884

Other (OTH)

AF:

0.000618

AC:

AN:

43666

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

139

186

232

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

110

<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:

0.000887

AC:

135

AN:

152264

Hom.:

Cov.:

AF XY:

0.000819

AC XY:

AN XY:

74464

show subpopulations

African (AFR)

AF:

0.000120

AC:

AN:

41556

American (AMR)

AF:

0.000720

AC:

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.000288

AC:

AN:

3468

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.00290

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10616

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00109

AC:

AN:

68028

Other (OTH)

AF:

0.00379

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.000106

Hom.:

Bravo

AF:

0.000926

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.28

(source)

DANN

Benign

0.66

PhyloP100

-0.53

Splicing

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