rs1157239

Variant names:

• chr12-65134947-C-A
• rs1157239
• ENST00000536787.2:n.260C>A

Your query was ambiguous. Multiple possible variants found:

• chr12-65134947-C-A
• chr12-65134947-C-G
• chr12-65134947-C-T

Variant summary

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

The ENST00000536787.2(APOOP3):​n.260C>A variant causes a non coding transcript exon 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)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: APOOP3 ENST00000536787.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.752
• Publications: 10 publications found

Genes affected

APOOP3 (HGNC:48741): (apolipoprotein O pseudogene 3)

ENSG00000289319 (HGNC:):

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=-0.34).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000536787.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOOP3	ENST00000536787.2	TSL:6	n.260C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289319	ENST00000844184.1		n.164-11897G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 273420 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 157400

African (AFR) AF: 0.00 AC: 0 AN: 8834

American (AMR) AF: 0.00 AC: 0 AN: 25922

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6280

East Asian (EAS) AF: 0.00 AC: 0 AN: 9878

South Asian (SAS) AF: 0.00 AC: 0 AN: 48304

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16670

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 794

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 144550

Other (OTH) AF: 0.00 AC: 0 AN: 12188

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	9.8
DANN	Benign	0.81
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs1157239; hg19: chr12-65528727;