3-88459217-G-C

Variant summary

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

The NM_001368165.1(CSNKA2IP):c.-270-5871G>C 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: CSNKA2IP NM_001368165.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.710

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 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/exons	MANE	UniProt
CSNKA2IP	NM_001368165.1	c.-270-5871G>C		intron_variant		ENST00000637986.2
CSNKA2IP	NM_001368166.1	c.-270-5871G>C		intron_variant
CSNKA2IP	NM_001368167.1	c.-270-5871G>C		intron_variant
CSNKA2IP	NM_001368168.1	c.-270-5871G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CSNKA2IP	ENST00000637986.2	c.-270-5871G>C		intron_variant		4	NM_001368165.1	P1
CSNKA2IP	ENST00000635844.1	n.393-5871G>C		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000636323.1	n.355-5871G>C		intron_variant, non_coding_transcript_variant		4
CSNKA2IP	ENST00000638109.1	n.317-5871G>C		intron_variant, non_coding_transcript_variant		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	1.2
Dann	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1982562; hg19: chr3-88508367;