3-88431940-A-T

Variant names:

• chr3-88431940-A-T
• rs6795028
• NM_001368165.1:c.-270-33148A>T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001368165.1(CSNK2A2IP):​c.-270-33148A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CSNK2A2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162

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 Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CSNK2A2IP	NM_001368165.1	c.-270-33148A>T		intron_variant	Intron 1 of 1	ENST00000637986.2	NP_001355094.1
CSNK2A2IP	NM_001368166.1	c.-271+32157A>T		intron_variant	Intron 2 of 2		NP_001355095.1
CSNK2A2IP	NM_001368167.1	c.-270-33148A>T		intron_variant	Intron 2 of 2		NP_001355096.1
CSNK2A2IP	NM_001368168.1	c.-271+32114A>T		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.-270-33148A>T		intron_variant	Intron 1 of 1	4	NM_001368165.1	ENSP00000489704.1
CSNKA2IP	ENST00000635844.1	n.392+32114A>T		intron_variant	Intron 2 of 2	4
CSNKA2IP	ENST00000636323.1	n.354+32157A>T		intron_variant	Intron 2 of 2	4
CSNKA2IP	ENST00000638109.1	n.317-33148A>T		intron_variant	Intron 2 of 2	4

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.1
DANN	Benign	0.74

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;