3-88463389-T-C

Variant names:

• chr3-88463389-T-C
• rs17559005
• NM_001368165.1:c.-270-1699T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001368165.1(CSNK2A2IP):​c.-270-1699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.293 in 152,006 control chromosomes in the GnomAD database, including 7,242 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 0.29 (7242 hom., cov: 31)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623
• Publications: 0 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK2A2IP	NM_001368165.1	MANE Select	c.-270-1699T>C		intron	N/A	NP_001355094.1
	CSNK2A2IP	NM_001368166.1		c.-270-1699T>C		intron	N/A	NP_001355095.1
	CSNK2A2IP	NM_001368167.1		c.-270-1699T>C		intron	N/A	NP_001355096.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK2A2IP	ENST00000637986.2	TSL:4 MANE Select	c.-270-1699T>C		intron	N/A	ENSP00000489704.1
	CSNK2A2IP	ENST00000635844.1	TSL:4	n.393-1699T>C		intron	N/A
	CSNK2A2IP	ENST00000636323.1	TSL:4	n.355-1699T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44441 AN: 151888 Hom.: 7231 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.318

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.293 AC: 44475 AN: 152006 Hom.: 7242 Cov.: 31 AF XY: 0.302 AC XY: 22426 AN XY: 74284

African (AFR) AF: 0.175 AC: 7272 AN: 41472

American (AMR) AF: 0.452 AC: 6891 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1272 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2487 AN: 5178

South Asian (SAS) AF: 0.288 AC: 1392 AN: 4826

European-Finnish (FIN) AF: 0.398 AC: 4195 AN: 10536

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19796 AN: 67958

Other (OTH) AF: 0.314 AC: 662 AN: 2110

Alfa AF: 0.309 Hom.: 1368

Bravo AF: 0.298

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.47
DANN	Benign	0.41
PhyloP100		-0.62

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17559005; hg19: chr3-88512539;