rs6809413

Variant names:

• chr3-88463299-G-A
• rs6809413
• NM_001368165.1:c.-270-1789G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-88463299-G-A
• chr3-88463299-G-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.-270-1789G>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 149,854 control chromosomes in the GnomAD database, including 11,020 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 (11020 hom., cov: 28)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A2IP	NM_001368165.1	c.-270-1789G>A		intron_variant	Intron 1 of 1	ENST00000637986.2	NP_001355094.1
CSNK2A2IP	NM_001368166.1	c.-270-1789G>A		intron_variant	Intron 2 of 2		NP_001355095.1
CSNK2A2IP	NM_001368167.1	c.-270-1789G>A		intron_variant	Intron 2 of 2		NP_001355096.1
CSNK2A2IP	NM_001368168.1	c.-270-1789G>A		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.-270-1789G>A		intron_variant	Intron 1 of 1	4	NM_001368165.1	ENSP00000489704.1
CSNK2A2IP	ENST00000635844.1	n.393-1789G>A		intron_variant	Intron 2 of 2	4
CSNK2A2IP	ENST00000636323.1	n.355-1789G>A		intron_variant	Intron 2 of 2	4
CSNK2A2IP	ENST00000638109.1	n.317-1789G>A		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56185 AN: 149742 Hom.: 10992 Cov.: 28

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.490

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.686

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.474

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.375 AC: 56261 AN: 149854 Hom.: 11020 Cov.: 28 AF XY: 0.385 AC XY: 28039 AN XY: 72922

African (AFR) AF: 0.369 AC: 15052 AN: 40782

American (AMR) AF: 0.491 AC: 7403 AN: 15080

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1348 AN: 3456

East Asian (EAS) AF: 0.687 AC: 3503 AN: 5096

South Asian (SAS) AF: 0.372 AC: 1766 AN: 4744

European-Finnish (FIN) AF: 0.423 AC: 4168 AN: 9862

Middle Eastern (MID) AF: 0.469 AC: 135 AN: 288

European-Non Finnish (NFE) AF: 0.321 AC: 21673 AN: 67552

Other (OTH) AF: 0.394 AC: 821 AN: 2084

Alfa AF: 0.370 Hom.: 1945

Bravo AF: 0.386

Asia WGS AF: 0.538 AC: 1867 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.10
DANN	Benign	0.23
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs6809413; hg19: chr3-88512449;