rs17559005

Positions:

• chr3-88463389-T-C

Variant summary

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

The NM_001368165.1(CSNKA2IP):​c.-270-1699T>C 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 152,006 control chromosomes in the GnomAD database, including 7,242 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 (7242 hom., cov: 31)
• Consequence: CSNKA2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.623

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.465 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNKA2IP	NM_001368165.1	c.-270-1699T>C		intron_variant		ENST00000637986.2
CSNKA2IP	NM_001368166.1	c.-270-1699T>C		intron_variant
CSNKA2IP	NM_001368167.1	c.-270-1699T>C		intron_variant
CSNKA2IP	NM_001368168.1	c.-270-1699T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNKA2IP	ENST00000637986.2	c.-270-1699T>C		intron_variant		4	NM_001368165.1	P1
CSNKA2IP	ENST00000635844.1	n.393-1699T>C		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000636323.1	n.355-1699T>C		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000638109.1	n.317-1699T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44441 AN: 151888 Hom.: 7231 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: 0.480

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.293 AC: 44475 AN: 152006 Hom.: 7242 Cov.: 31 AF XY: 0.302 AC XY: 22426 AN XY: 74284

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.452

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.480

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.291

Gnomad4 OTH AF: 0.314

Alfa AF: 0.313 Hom.: 1350

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	-0.92
CADD	Benign	0.47
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17559005; hg19: chr3-88512539;