rs2930770

Variant names:

• chr22-21483071-C-G
• rs2930770
• ENST00000462560.6:n.697G>C

Your query was ambiguous. Multiple possible variants found:

• chr22-21483071-C-G
• chr22-21483071-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000462560.6(ENSG00000293427):​n.697G>C variant causes a non coding transcript exon change involving the alteration of a 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: 16)
• Consequence: ENSG00000293427 ENST00000462560.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.35
• Publications: 2 publications found

Genes affected

ENSG00000293427 (HGNC:):

PI4KAP2 (HGNC:33577): (phosphatidylinositol 4-kinase alpha pseudogene 2) Predicted to enable 1-phosphatidylinositol 4-kinase activity. Predicted to be involved in phosphatidylinositol phosphate biosynthetic process and phosphatidylinositol-mediated signaling. Predicted to be active in cytoplasm and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000462560.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PI4KAP2	NR_003700.1		n.964G>C		non_coding_transcript_exon	Exon 8 of 17

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293427	ENST00000462560.6	TSL:1	n.697G>C		non_coding_transcript_exon	Exon 6 of 15
	ENSG00000293427	ENST00000479693.1	TSL:1	n.993G>C		non_coding_transcript_exon	Exon 8 of 13
	PI4KAP2	ENST00000360806.9	TSL:6	n.673G>C		non_coding_transcript_exon	Exon 6 of 16

Frequencies

GnomAD3 genomes Cov.: 16

GnomAD4 exome Cov.: 24

GnomAD4 genome Cov.: 16

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	21
DANN	Benign	0.86
PhyloP100		7.3

Splicing

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

Other links and lift over

dbSNP: rs2930770; hg19: chr22-21837360;