3-88431940-A-G

Variant names:

• chr3-88431940-A-G
• rs6795028
• NM_001368165.1:c.-270-33148A>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.-270-33148A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,898 control chromosomes in the GnomAD database, including 21,406 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 0.51 (21406 hom., cov: 32)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.619 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A2IP	NM_001368165.1	c.-270-33148A>G		intron_variant	Intron 1 of 1	ENST00000637986.2	NP_001355094.1
CSNK2A2IP	NM_001368166.1	c.-271+32157A>G		intron_variant	Intron 2 of 2		NP_001355095.1
CSNK2A2IP	NM_001368167.1	c.-270-33148A>G		intron_variant	Intron 2 of 2		NP_001355096.1
CSNK2A2IP	NM_001368168.1	c.-271+32114A>G		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.-270-33148A>G		intron_variant	Intron 1 of 1	4	NM_001368165.1	ENSP00000489704.1
CSNK2A2IP	ENST00000635844.1	n.392+32114A>G		intron_variant	Intron 2 of 2	4
CSNK2A2IP	ENST00000636323.1	n.354+32157A>G		intron_variant	Intron 2 of 2	4
CSNK2A2IP	ENST00000638109.1	n.317-33148A>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78166 AN: 151780 Hom.: 21394 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.521

Gnomad SAS AF: 0.567

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.510

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

GnomAD4 genome AF: 0.515 AC: 78197 AN: 151898 Hom.: 21406 Cov.: 32 AF XY: 0.508 AC XY: 37726 AN XY: 74228

African (AFR) AF: 0.354 AC: 14678 AN: 41464

American (AMR) AF: 0.439 AC: 6710 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1889 AN: 3470

East Asian (EAS) AF: 0.520 AC: 2680 AN: 5154

South Asian (SAS) AF: 0.568 AC: 2743 AN: 4826

European-Finnish (FIN) AF: 0.516 AC: 5416 AN: 10506

Middle Eastern (MID) AF: 0.510 AC: 149 AN: 292

European-Non Finnish (NFE) AF: 0.624 AC: 42366 AN: 67888

Other (OTH) AF: 0.514 AC: 1083 AN: 2106

Alfa AF: 0.590 Hom.: 42358

Bravo AF: 0.500

Asia WGS AF: 0.549 AC: 1903 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.83
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs6795028; hg19: chr3-88481090;