3-88459217-G-A

Variant names:

• chr3-88459217-G-A
• rs1982562
• NM_001368165.1:c.-270-5871G>A

Variant summary

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

The NM_001368165.1(CSNK2A2IP):​c.-270-5871G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,884 control chromosomes in the GnomAD database, including 11,204 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 0.38 (11204 hom., cov: 32)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710
• 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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CSNK2A2IP	NM_001368165.1	MANE Select	c.-270-5871G>A		intron	N/A	NP_001355094.1	A0A1B0GTH6
	CSNK2A2IP	NM_001368166.1		c.-270-5871G>A		intron	N/A	NP_001355095.1	A0A1B0GTH6
	CSNK2A2IP	NM_001368167.1		c.-270-5871G>A		intron	N/A	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.-270-5871G>A		intron	N/A	ENSP00000489704.1	A0A1B0GTH6
	CSNK2A2IP	ENST00000635844.1	TSL:4	n.393-5871G>A		intron	N/A
	CSNK2A2IP	ENST00000636323.1	TSL:4	n.355-5871G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56902 AN: 151768 Hom.: 11175 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.375 AC: 56981 AN: 151884 Hom.: 11204 Cov.: 32 AF XY: 0.384 AC XY: 28480 AN XY: 74214

African (AFR) AF: 0.369 AC: 15280 AN: 41428

American (AMR) AF: 0.490 AC: 7485 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3468

East Asian (EAS) AF: 0.687 AC: 3548 AN: 5166

South Asian (SAS) AF: 0.373 AC: 1797 AN: 4822

European-Finnish (FIN) AF: 0.419 AC: 4409 AN: 10524

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.320 AC: 21752 AN: 67902

Other (OTH) AF: 0.393 AC: 827 AN: 2104

Alfa AF: 0.289 Hom.: 1123

Bravo AF: 0.386

Asia WGS AF: 0.537 AC: 1863 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.12
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs1982562; hg19: chr3-88508367;