rs6809413

chr3-88463299-G-Achr3-88463299-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001368165.1(CSNKA2IP):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: CSNKA2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

Genes affected

CSNKA2IP (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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CSNKA2IP	NM_001368165.1	c.-270-1789G>A		intron_variant		ENST00000637986.2
CSNKA2IP	NM_001368166.1	c.-270-1789G>A		intron_variant
CSNKA2IP	NM_001368167.1	c.-270-1789G>A		intron_variant
CSNKA2IP	NM_001368168.1	c.-270-1789G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNKA2IP	ENST00000637986.2	c.-270-1789G>A		intron_variant		4	NM_001368165.1	P1
CSNKA2IP	ENST00000635844.1	n.393-1789G>A		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000636323.1	n.355-1789G>A		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000638109.1	n.317-1789G>A		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.369

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.687

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.423

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.394

Alfa AF: 0.370 Hom.: 1891

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6809413; hg19: chr3-88512449;