3-88458699-T-C

Variant names:

• chr3-88458699-T-C
• rs13101122
• NM_001368165.1:c.-270-6389T>C

Variant summary

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

The NM_001368165.1(CSNK2A2IP):​c.-270-6389T>C 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 151,924 control chromosomes in the GnomAD database, including 11,199 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 0.37 (11199 hom., cov: 32)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A2IP	NM_001368165.1	c.-270-6389T>C		intron_variant	Intron 1 of 1	ENST00000637986.2	NP_001355094.1
CSNK2A2IP	NM_001368166.1	c.-270-6389T>C		intron_variant	Intron 2 of 2		NP_001355095.1
CSNK2A2IP	NM_001368167.1	c.-270-6389T>C		intron_variant	Intron 2 of 2		NP_001355096.1
CSNK2A2IP	NM_001368168.1	c.-270-6389T>C		intron_variant	Intron 2 of 2		NP_001355097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNKA2IP	ENST00000637986.2	c.-270-6389T>C		intron_variant	Intron 1 of 1	4	NM_001368165.1	ENSP00000489704.1
CSNKA2IP	ENST00000635844.1	n.393-6389T>C		intron_variant	Intron 2 of 2	4
CSNKA2IP	ENST00000636323.1	n.355-6389T>C		intron_variant	Intron 2 of 2	4
CSNKA2IP	ENST00000638109.1	n.317-6389T>C		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56889 AN: 151806 Hom.: 11170 Cov.: 32

Gnomad AFR AF: 0.368

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.373

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.320

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.375 AC: 56969 AN: 151924 Hom.: 11199 Cov.: 32 AF XY: 0.384 AC XY: 28492 AN XY: 74242

Gnomad4 AFR AF: 0.368

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.390

Gnomad4 EAS AF: 0.685

Gnomad4 SAS AF: 0.373

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.320

Gnomad4 OTH AF: 0.393

Alfa AF: 0.334 Hom.: 15751

Bravo AF: 0.386

Asia WGS AF: 0.537 AC: 1863 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13101122; hg19: chr3-88507849;