3-88458699-T-C

Variant names:

• chr3-88458699-T-C
• rs13101122
• NM_001368165.1:c.-270-6389T>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.-270-6389T>C 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 151,924 control chromosomes in the GnomAD database, including 11,199 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 0.37 (11199 hom., cov: 32)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 1 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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 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.-270-6389T>C		intron	N/A	NP_001355094.1
	CSNK2A2IP	NM_001368166.1		c.-270-6389T>C		intron	N/A	NP_001355095.1
	CSNK2A2IP	NM_001368167.1		c.-270-6389T>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.-270-6389T>C		intron	N/A	ENSP00000489704.1
	CSNK2A2IP	ENST00000635844.1	TSL:4	n.393-6389T>C		intron	N/A
	CSNK2A2IP	ENST00000636323.1	TSL:4	n.355-6389T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56889 AN: 151806 Hom.: 11170 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.375 AC: 56969 AN: 151924 Hom.: 11199 Cov.: 32 AF XY: 0.384 AC XY: 28492 AN XY: 74242

African (AFR) AF: 0.368 AC: 15266 AN: 41430

American (AMR) AF: 0.490 AC: 7478 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1351 AN: 3468

East Asian (EAS) AF: 0.685 AC: 3537 AN: 5162

South Asian (SAS) AF: 0.373 AC: 1798 AN: 4824

European-Finnish (FIN) AF: 0.420 AC: 4420 AN: 10532

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

European-Non Finnish (NFE) AF: 0.320 AC: 21761 AN: 67944

Other (OTH) AF: 0.393 AC: 827 AN: 2106

Alfa AF: 0.339 Hom.: 32996

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	-1.0
CADD	Benign	0.24
DANN	Benign	0.50
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs13101122; hg19: chr3-88507849;