rs10511137

Variant names:

• chr3-88463052-A-G
• rs10511137
• NM_001368165.1:c.-270-2036A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001368165.1(CSNK2A2IP):​c.-270-2036A>G 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 152,104 control chromosomes in the GnomAD database, including 7,257 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 (7257 hom., cov: 32)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A2IP	NM_001368165.1	c.-270-2036A>G		intron_variant	Intron 1 of 1	ENST00000637986.2	NP_001355094.1
CSNK2A2IP	NM_001368166.1	c.-270-2036A>G		intron_variant	Intron 2 of 2		NP_001355095.1
CSNK2A2IP	NM_001368167.1	c.-270-2036A>G		intron_variant	Intron 2 of 2		NP_001355096.1
CSNK2A2IP	NM_001368168.1	c.-270-2036A>G		intron_variant	Intron 2 of 2		NP_001355097.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CSNK2A2IP	ENST00000637986.2	c.-270-2036A>G		intron_variant	Intron 1 of 1	4	NM_001368165.1	ENSP00000489704.1
CSNK2A2IP	ENST00000635844.1	n.393-2036A>G		intron_variant	Intron 2 of 2	4
CSNK2A2IP	ENST00000636323.1	n.355-2036A>G		intron_variant	Intron 2 of 2	4
CSNK2A2IP	ENST00000638109.1	n.317-2036A>G		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes AF: 0.293 AC: 44462 AN: 151986 Hom.: 7246 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.431

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.289

Gnomad FIN AF: 0.400

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.291

Gnomad OTH AF: 0.317

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

GnomAD4 genome AF: 0.293 AC: 44496 AN: 152104 Hom.: 7257 Cov.: 32 AF XY: 0.302 AC XY: 22441 AN XY: 74336

African (AFR) AF: 0.175 AC: 7271 AN: 41526

American (AMR) AF: 0.452 AC: 6901 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3468

East Asian (EAS) AF: 0.479 AC: 2476 AN: 5170

South Asian (SAS) AF: 0.288 AC: 1392 AN: 4830

European-Finnish (FIN) AF: 0.400 AC: 4217 AN: 10552

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.291 AC: 19798 AN: 67970

Other (OTH) AF: 0.314 AC: 663 AN: 2114

Alfa AF: 0.298 Hom.: 2035

Bravo AF: 0.298

Asia WGS AF: 0.368 AC: 1278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.78
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs10511137; hg19: chr3-88512202;