12-65134947-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000536787.2(APOOP3):​n.260C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 416,078 control chromosomes in the GnomAD database, including 74,778 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 0.56 (26567 hom., cov: 32)
  • Exomes 𝑓: 0.59 (48211 hom.)
• 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: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

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>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000289319	ENST00000844184.1		n.164-11897G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85490 AN: 151912 Hom.: 26568 Cov.: 32

Gnomad AFR AF: 0.283

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.568

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.874

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.695

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.673

Gnomad OTH AF: 0.625

GnomAD4 exome AF: 0.590 AC: 155747 AN: 264048 Hom.: 48211 Cov.: 0 AF XY: 0.591 AC XY: 89568 AN XY: 151640

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.231 AC: 1985 AN: 8598

American (AMR) AF: 0.486 AC: 12101 AN: 24898

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 3707 AN: 6018

East Asian (EAS) AF: 0.845 AC: 8214 AN: 9722

South Asian (SAS) AF: 0.533 AC: 24912 AN: 46772

European-Finnish (FIN) AF: 0.639 AC: 10442 AN: 16330

Middle Eastern (MID) AF: 0.633 AC: 480 AN: 758

European-Non Finnish (NFE) AF: 0.623 AC: 86780 AN: 139188

Other (OTH) AF: 0.606 AC: 7126 AN: 11764

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.562 AC: 85514 AN: 152030 Hom.: 26567 Cov.: 32 AF XY: 0.567 AC XY: 42151 AN XY: 74308

African (AFR) AF: 0.284 AC: 11757 AN: 41444

American (AMR) AF: 0.568 AC: 8661 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.710 AC: 2464 AN: 3472

East Asian (EAS) AF: 0.874 AC: 4521 AN: 5172

South Asian (SAS) AF: 0.609 AC: 2942 AN: 4828

European-Finnish (FIN) AF: 0.695 AC: 7330 AN: 10554

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.673 AC: 45770 AN: 67986

Other (OTH) AF: 0.619 AC: 1306 AN: 2110

Alfa AF: 0.651 Hom.: 14259

Bravo AF: 0.545

Asia WGS AF: 0.690 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	11
DANN	Benign	0.78
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;