Genetic Variant PTOV1:c.1041+291T>A (chr19-49858944-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001394010.1(PTOV1):c.1041+291T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 305,792 control chromosomes in the GnomAD database, including 22,342 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 0.39 ( 11876 hom., cov: 33)

Exomes 𝑓: 0.36 ( 10466 hom. )

Consequence

PTOV1
NM_001394010.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.46

Publications

6 publications found

Variant links:

Genes affected

PTOV1 (HGNC:9632): (PTOV1 extended AT-hook containing adaptor protein) This gene encodes a protein that was found to be overexpressed in prostate adenocarcinomas. The encoded protein was found to interact with the lipid raft protein flotillin-1 and shuttle it from the cytoplasm to the nucleus in a cell cycle dependent manner. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Feb 2015]

PTOV1 links:

PTOV1-AS2 (HGNC:51284): (PTOV1 antisense RNA 2)

PTOV1-AS2 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394010.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PTOV1	NM_001394010.1	MANE Select	c.1041+291T>A	intron	N/A	NP_001380939.1
PTOV1-AS2	NR_110730.1		n.238A>T	non_coding_transcript_exon	Exon 2 of 5
PTOV1	NM_001364747.2		c.1086+291T>A	intron	N/A	NP_001351676.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PTOV1	ENST00000391842.6	TSL:5 MANE Select	c.1041+291T>A	intron	N/A	ENSP00000375717.1
PTOV1	ENST00000599732.5	TSL:1	c.1041+291T>A	intron	N/A	ENSP00000469128.1
PTOV1	ENST00000601675.5	TSL:1	c.1041+291T>A	intron	N/A	ENSP00000472816.1

Frequencies

GnomAD3 genomes

AF:

0.387

AC:

58745

AN:

151946

Hom.:

11852

Cov.:

show subpopulations

Gnomad AFR

AF:

0.482

Gnomad AMI

AF:

0.310

Gnomad AMR

AF:

0.370

Gnomad ASJ

AF:

0.431

Gnomad EAS

AF:

0.427

Gnomad SAS

AF:

0.493

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.440

Gnomad NFE

AF:

0.346

Gnomad OTH

AF:

0.378

GnomAD4 exome

AF:

0.363

AC:

55875

AN:

153728

Hom.:

10466

Cov.:

AF XY:

0.366

AC XY:

28817

AN XY:

78668

show subpopulations

African (AFR)

AF:

0.477

AC:

2710

AN:

5682

American (AMR)

AF:

0.341

AC:

2221

AN:

6522

Ashkenazi Jewish (ASJ)

AF:

0.431

AC:

2528

AN:

5862

East Asian (EAS)

AF:

0.402

AC:

5455

AN:

13576

South Asian (SAS)

AF:

0.476

AC:

3092

AN:

6492

European-Finnish (FIN)

AF:

0.240

AC:

2323

AN:

9692

Middle Eastern (MID)

AF:

0.471

AC:

369

AN:

784

European-Non Finnish (NFE)

AF:

0.351

AC:

33395

AN:

95212

Other (OTH)

AF:

0.382

AC:

3782

AN:

9906

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1691

3382

5073

6764

8455

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

246

492

738

984

1230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.387

AC:

58812

AN:

152064

Hom.:

11876

Cov.:

AF XY:

0.384

AC XY:

28552

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.482

AC:

19978

AN:

41456

American (AMR)

AF:

0.370

AC:

5654

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.431

AC:

1497

AN:

3470

East Asian (EAS)

AF:

0.427

AC:

2207

AN:

5172

South Asian (SAS)

AF:

0.493

AC:

2375

AN:

4818

European-Finnish (FIN)

AF:

0.226

AC:

2387

AN:

10582

Middle Eastern (MID)

AF:

0.435

AC:

128

AN:

294

European-Non Finnish (NFE)

AF:

0.346

AC:

23495

AN:

67956

Other (OTH)

AF:

0.383

AC:

809

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1884

3768

5651

7535

9419

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

568

1136

1704

2272

2840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.345

Hom.:

1176

Bravo

AF:

0.396

Asia WGS

AF:

0.469

AC:

1630

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.37

(source)

DANN

Benign

0.85

PhyloP100

-2.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over