rs12107308

Variant names:

• chr3-88433203-C-G
• rs12107308
• NM_001368165.1:c.-270-31885C>G

Variant summary

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

The NM_001368165.1(CSNK2A2IP):​c.-270-31885C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,804 control chromosomes in the GnomAD database, including 2,987 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 0.19 (2987 hom., cov: 32)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 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.-270-31885C>G		intron	N/A	NP_001355094.1
	CSNK2A2IP	NM_001368166.1		c.-270-31885C>G		intron	N/A	NP_001355095.1
	CSNK2A2IP	NM_001368167.1		c.-270-31885C>G		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.-270-31885C>G		intron	N/A	ENSP00000489704.1
	CSNK2A2IP	ENST00000635844.1	TSL:4	n.393-31885C>G		intron	N/A
	CSNK2A2IP	ENST00000636323.1	TSL:4	n.355-31885C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29101 AN: 151686 Hom.: 2986 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.192 AC: 29129 AN: 151804 Hom.: 2987 Cov.: 32 AF XY: 0.195 AC XY: 14443 AN XY: 74164

African (AFR) AF: 0.230 AC: 9505 AN: 41410

American (AMR) AF: 0.135 AC: 2065 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.178 AC: 619 AN: 3468

East Asian (EAS) AF: 0.205 AC: 1060 AN: 5176

South Asian (SAS) AF: 0.166 AC: 801 AN: 4820

European-Finnish (FIN) AF: 0.274 AC: 2871 AN: 10482

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11496 AN: 67882

Other (OTH) AF: 0.179 AC: 377 AN: 2110

Alfa AF: 0.180 Hom.: 325

Bravo AF: 0.184

Asia WGS AF: 0.179 AC: 617 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.62
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs12107308; hg19: chr3-88482353;