Variant 3-88465948-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

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 id is 2653988.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
CSNK2A2IP	NM_001368165.1 link	c.591C>T	p.Ile197Ile	synonymous_variant	2/2	ENST00000637986.2	NP_001355094.1
CSNK2A2IP	NM_001368166.1 link	c.591C>T	p.Ile197Ile	synonymous_variant	3/3		NP_001355095.1
CSNK2A2IP	NM_001368167.1 link	c.591C>T	p.Ile197Ile	synonymous_variant	3/3		NP_001355096.1
CSNK2A2IP	NM_001368168.1 link	c.591C>T	p.Ile197Ile	synonymous_variant	3/3		NP_001355097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CSNKA2IP	ENST00000637986.2 link	c.591C>T	p.Ile197Ile	synonymous_variant	2/2	4	NM_001368165.1	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

Gnomad4 AFR exome

AF:

0.0000435

Gnomad4 AMR exome

AF:

0.000594

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000754

Gnomad4 SAS exome

AF:

0.00287

Gnomad4 FIN exome

AF:

0.000190

Gnomad4 NFE exome

AF:

0.000591

Gnomad4 OTH exome

AF:

0.000618

GnomAD4 genome

AF:

0.000887

AC:

135

AN:

152264

Hom.:

Cov.:

AF XY:

0.000819

AC XY:

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.000120

Gnomad4 AMR

AF:

0.000720

Gnomad4 ASJ

AF:

0.000288

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00109

Gnomad4 OTH

AF:

0.00379

Alfa

AF:

0.000106

Hom.:

Bravo

AF:

0.000926

Asia WGS

AF:

0.00115

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jul 01, 2022

CSNKA2IP: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.28

DANN

Benign

0.66

Splicing

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