dbSNP rs7257463: 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 ENST00000391842.6(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
ENST00000391842.6 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:

Genome browser will be placed here

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein
PTOV1-AS2	NR_110730.1 link	n.238A>T	non_coding_transcript_exon_variant	Exon 2 of 5
PTOV1	NM_001364747.2 link	c.1086+291T>A	intron_variant	Intron 10 of 12	NP_001351676.1
PTOV1	NM_001364749.2 link	c.1086+291T>A	intron_variant	Intron 10 of 12	NP_001351678.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTOV1	ENST00000391842.6 link	c.1041+291T>A		intron_variant	Intron 10 of 11	5		ENSP00000375717.1		Q86YD1-1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over