rs12107308

chr3-88433203-C-G

Variant summary

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

The NM_001368165.1(CSNKA2IP):c.-270-31885C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,804 control chromosomes in the GnomAD database, including 2,987 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 0.19 (2987 hom., cov: 32)
• Consequence: CSNKA2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.226 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CSNKA2IP	NM_001368165.1	c.-270-31885C>G		intron_variant		ENST00000637986.2
CSNKA2IP	NM_001368166.1	c.-270-31885C>G		intron_variant
CSNKA2IP	NM_001368167.1	c.-270-31885C>G		intron_variant
CSNKA2IP	NM_001368168.1	c.-270-31885C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNKA2IP	ENST00000637986.2	c.-270-31885C>G		intron_variant		4	NM_001368165.1	P1
CSNKA2IP	ENST00000635844.1	n.393-31885C>G		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000636323.1	n.355-31885C>G		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000638109.1	n.317-31885C>G		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29101 AN: 151686 Hom.: 2986 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.178

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.192 AC: 29129 AN: 151804 Hom.: 2987 Cov.: 32 AF XY: 0.195 AC XY: 14443 AN XY: 74164

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.178

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.166

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.169

Gnomad4 OTH AF: 0.179

Alfa AF: 0.180 Hom.: 325

Bravo AF: 0.184

Asia WGS AF: 0.179 AC: 617 AN: 3442

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.29
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12107308; hg19: chr3-88482353;