rs6795028

chr3-88431940-A-Gchr3-88431940-A-T

Variant summary

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

The NM_001368165.1(CSNKA2IP):c.-270-33148A>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: CSNKA2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

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=-0.9).
• 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/exons	MANE	UniProt
CSNKA2IP	NM_001368165.1	c.-270-33148A>G		intron_variant		ENST00000637986.2
CSNKA2IP	NM_001368166.1	c.-271+32157A>G		intron_variant
CSNKA2IP	NM_001368167.1	c.-270-33148A>G		intron_variant
CSNKA2IP	NM_001368168.1	c.-271+32114A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNKA2IP	ENST00000637986.2	c.-270-33148A>G		intron_variant		4	NM_001368165.1	P1
CSNKA2IP	ENST00000635844.1	n.392+32114A>G		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000636323.1	n.354+32157A>G		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000638109.1	n.317-33148A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.439

Gnomad4 ASJ AF: 0.544

Gnomad4 EAS AF: 0.520

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.624

Gnomad4 OTH AF: 0.514

Alfa AF: 0.592 Hom.: 36104

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6795028; hg19: chr3-88481090;