3-88463472-C-T

Variant names:

• chr3-88463472-C-T
• rs33966381
• NM_001368165.1:c.-270-1616C>T

Variant summary

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

The NM_001368165.1(CSNK2A2IP):​c.-270-1616C>T 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 151,956 control chromosomes in the GnomAD database, including 7,260 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 (7260 hom., cov: 31)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.23
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.464 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A2IP	NM_001368165.1	c.-270-1616C>T		intron_variant	Intron 1 of 1	ENST00000637986.2	NP_001355094.1
CSNK2A2IP	NM_001368166.1	c.-270-1616C>T		intron_variant	Intron 2 of 2		NP_001355095.1
CSNK2A2IP	NM_001368167.1	c.-270-1616C>T		intron_variant	Intron 2 of 2		NP_001355096.1
CSNK2A2IP	NM_001368168.1	c.-270-1616C>T		intron_variant	Intron 2 of 2		NP_001355097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK2A2IP	ENST00000637986.2	c.-270-1616C>T		intron_variant	Intron 1 of 1	4	NM_001368165.1	ENSP00000489704.1
CSNK2A2IP	ENST00000635844.1	n.393-1616C>T		intron_variant	Intron 2 of 2	4
CSNK2A2IP	ENST00000636323.1	n.355-1616C>T		intron_variant	Intron 2 of 2	4
CSNK2A2IP	ENST00000638109.1	n.317-1616C>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44459 AN: 151838 Hom.: 7249 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: 0.479

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.293 AC: 44493 AN: 151956 Hom.: 7260 Cov.: 31 AF XY: 0.302 AC XY: 22429 AN XY: 74242

African (AFR) AF: 0.175 AC: 7272 AN: 41450

American (AMR) AF: 0.453 AC: 6905 AN: 15258

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

East Asian (EAS) AF: 0.480 AC: 2478 AN: 5166

South Asian (SAS) AF: 0.288 AC: 1386 AN: 4814

European-Finnish (FIN) AF: 0.400 AC: 4209 AN: 10532

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

European-Non Finnish (NFE) AF: 0.291 AC: 19804 AN: 67954

Other (OTH) AF: 0.314 AC: 661 AN: 2108

Alfa AF: 0.282 Hom.: 863

Bravo AF: 0.298

Asia WGS AF: 0.368 AC: 1279 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.68
PhyloP100		-3.2

Splicing

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

Other links and lift over

dbSNP: rs33966381; hg19: chr3-88512622;