Variant chr6-138218046-A-AG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_021635.3(PBOV1):c.349dupC(p.Leu117fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 1,613,418 control chromosomes in the GnomAD database, including 8,837 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.11 ( 1314 hom., cov: 31)

Exomes 𝑓: 0.083 ( 7523 hom. )

Consequence

PBOV1
NM_021635.3 frameshift

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0220

Variant links:

Genes affected

PBOV1 (HGNC:21079): (prostate and breast cancer overexpressed 1) This intronless gene encodes a protein of unknown function. Its expression is up-regulated in some types of cancer, including prostate, breast, and bladder cancer. [provided by RefSeq, Aug 2011]

PBOV1 links:

ARFGEF3 (HGNC:21213): (ARFGEF family member 3) Predicted to enable guanyl-nucleotide exchange factor activity. Predicted to be involved in actin cytoskeleton organization. Predicted to be located in transport vesicle membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ARFGEF3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PBOV1	NM_021635.3 link	c.349dupC	p.Leu117fs	frameshift_variant	1/1	ENST00000527246.3	NP_067648.1	Q9GZY1
ARFGEF3	NM_020340.5 link	c.351+8008dupG		intron_variant		ENST00000251691.5	NP_065073.3	Q5TH69
ARFGEF3	XR_001743524.2 link	n.499+8008dupG		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PBOV1	ENST00000527246.3 link	c.349dupC	p.Leu117fs	frameshift_variant	1/1	6	NM_021635.3	ENSP00000432353.1		Q9GZY1
ARFGEF3	ENST00000251691.5 link	c.351+8008dupG		intron_variant		1	NM_020340.5	ENSP00000251691.4		Q5TH69

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17123

AN:

152040

Hom.:

1297

Cov.:

show subpopulations

Gnomad AFR

AF:

0.156

Gnomad AMI

AF:

0.00548

Gnomad AMR

AF:

0.136

Gnomad ASJ

AF:

0.0700

Gnomad EAS

AF:

0.358

Gnomad SAS

AF:

0.0691

Gnomad FIN

AF:

0.115

Gnomad MID

AF:

0.0506

Gnomad NFE

AF:

0.0694

Gnomad OTH

AF:

0.0994

GnomAD3 exomes

AF:

0.119

AC:

29755

AN:

250830

Hom.:

2883

AF XY:

0.108

AC XY:

14682

AN XY:

135538

show subpopulations

Gnomad AFR exome

AF:

0.159

Gnomad AMR exome

AF:

0.214

Gnomad ASJ exome

AF:

0.0634

Gnomad EAS exome

AF:

0.368

Gnomad SAS exome

AF:

0.0609

Gnomad FIN exome

AF:

0.118

Gnomad NFE exome

AF:

0.0653

Gnomad OTH exome

AF:

0.0927

GnomAD4 exome

AF:

0.0835

AC:

121996

AN:

1461260

Hom.:

7523

Cov.:

AF XY:

0.0818

AC XY:

59448

AN XY:

726924

show subpopulations

Gnomad4 AFR exome

AF:

0.160

Gnomad4 AMR exome

AF:

0.207

Gnomad4 ASJ exome

AF:

0.0671

Gnomad4 EAS exome

AF:

0.360

Gnomad4 SAS exome

AF:

0.0626

Gnomad4 FIN exome

AF:

0.111

Gnomad4 NFE exome

AF:

0.0668

Gnomad4 OTH exome

AF:

0.0892

GnomAD4 genome

AF:

0.113

AC:

17177

AN:

152158

Hom.:

1314

Cov.:

AF XY:

0.115

AC XY:

8568

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.156

Gnomad4 AMR

AF:

0.137

Gnomad4 ASJ

AF:

0.0700

Gnomad4 EAS

AF:

0.359

Gnomad4 SAS

AF:

0.0690

Gnomad4 FIN

AF:

0.115

Gnomad4 NFE

AF:

0.0695

Gnomad4 OTH

AF:

0.0993

Alfa

AF:

0.0839

Hom.:

545

Bravo

AF:

0.121

Asia WGS

AF:

0.180

AC:

625

AN:

3478

EpiCase

AF:

0.0631

EpiControl

AF:

0.0580

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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