dbSNP rs3786662: PTOV1:c.559-848A>T (chr19-49856127-A-T) – 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.559-848A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.12 in 152,228 control chromosomes in the GnomAD database, including 1,408 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 0.12 ( 1408 hom., cov: 32)

Exomes 𝑓: 0.17 ( 0 hom. )

Consequence

PTOV1
ENST00000391842.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.421

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:

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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.189 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	Protein	UniProt
PTOV1	NM_001364747.2 link	c.604-848A>T	intron_variant	Intron 5 of 12	NP_001351676.1
PTOV1	NM_001364749.2 link	c.604-848A>T	intron_variant	Intron 5 of 12	NP_001351678.1
PTOV1	NM_001305105.2 link	c.559-848A>T	intron_variant	Intron 5 of 12	NP_001292034.1	Q86YD1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTOV1	ENST00000391842.6 link	c.559-848A>T		intron_variant	Intron 5 of 11	5		ENSP00000375717.1		Q86YD1-1

Frequencies

GnomAD3 genomes

AF:

0.121

AC:

18336

AN:

152056

Hom.:

1407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0318

Gnomad AMI

AF:

0.159

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.0730

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.193

Gnomad NFE

AF:

0.159

Gnomad OTH

AF:

0.132

GnomAD4 exome

AF:

0.167

AC:

AN:

Hom.:

Cov.:

AF XY:

0.190

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.125

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.174

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.120

AC:

18334

AN:

152174

Hom.:

1408

Cov.:

AF XY:

0.122

AC XY:

9059

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0318

AC:

1321

AN:

41538

American (AMR)

AF:

0.121

AC:

1845

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

825

AN:

3468

East Asian (EAS)

AF:

0.0730

AC:

377

AN:

5166

South Asian (SAS)

AF:

0.200

AC:

962

AN:

4820

European-Finnish (FIN)

AF:

0.163

AC:

1727

AN:

10606

Middle Eastern (MID)

AF:

0.190

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.159

AC:

10800

AN:

67970

Other (OTH)

AF:

0.131

AC:

276

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

831

1662

2493

3324

4155

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

216

432

648

864

1080

<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:

0.136

Hom.:

200

Bravo

AF:

0.110

Asia WGS

AF:

0.127

AC:

441

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.81

(source)

DANN

Benign

0.70

PhyloP100

-0.42

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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