Variant 12-65134947-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.752

Variant links:

Genes affected

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

APOOP3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOOP3	ENST00000536787.2 linkuse as main transcript	n.260C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes

AF:

0.563

AC:

85490

AN:

151912

Hom.:

26568

Cov.:

show subpopulations

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.:

AF XY:

0.591

AC XY:

89568

AN XY:

151640

show subpopulations

Gnomad4 AFR exome

AF:

0.231

Gnomad4 AMR exome

AF:

0.486

Gnomad4 ASJ exome

AF:

0.616

Gnomad4 EAS exome

AF:

0.845

Gnomad4 SAS exome

AF:

0.533

Gnomad4 FIN exome

AF:

0.639

Gnomad4 NFE exome

AF:

0.623

Gnomad4 OTH exome

AF:

0.606

GnomAD4 genome

AF:

0.562

AC:

85514

AN:

152030

Hom.:

26567

Cov.:

AF XY:

0.567

AC XY:

42151

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.284

Gnomad4 AMR

AF:

0.568

Gnomad4 ASJ

AF:

0.710

Gnomad4 EAS

AF:

0.874

Gnomad4 SAS

AF:

0.609

Gnomad4 FIN

AF:

0.695

Gnomad4 NFE

AF:

0.673

Gnomad4 OTH

AF:

0.619

Alfa

AF:

0.639

Hom.:

7343

Bravo

AF:

0.545

Asia WGS

AF:

0.690

AC:

2395

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.40

CADD

Benign

DANN

Benign

0.78

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over