rs542896699

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The NM_017432.5(PTOV1):ā€‹c.116C>Gā€‹(p.Ala39Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,220,128 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: š‘“ 0.0066 ( 8 hom., cov: 32)
Exomes š‘“: 0.00061 ( 7 hom. )

Consequence

PTOV1
NM_017432.5 missense

Scores

1
17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.116
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-AS1 (HGNC:44174): (PTOV1 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.0020639002).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00656 (993/151296) while in subpopulation AFR AF= 0.0219 (904/41362). AF 95% confidence interval is 0.0207. There are 8 homozygotes in gnomad4. There are 480 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PTOV1NM_001305105.2 linkc.116C>G p.Ala39Gly missense_variant Exon 1 of 13 NP_001292034.1 Q86YD1-1
PTOV1NM_001394010.1 linkc.116C>G p.Ala39Gly missense_variant Exon 1 of 12 NP_001380939.1
PTOV1NM_017432.5 linkc.116C>G p.Ala39Gly missense_variant Exon 1 of 13 NP_059128.2 Q86YD1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PTOV1ENST00000391842.6 linkc.116C>G p.Ala39Gly missense_variant Exon 1 of 12 5 ENSP00000375717.1 Q86YD1-1

Frequencies

GnomAD3 genomes
AF:
0.00657
AC:
994
AN:
151188
Hom.:
9
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0219
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00401
Gnomad ASJ
AF:
0.00116
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000103
Gnomad OTH
AF:
0.00819
GnomAD4 exome
AF:
0.000610
AC:
652
AN:
1068832
Hom.:
7
Cov.:
31
AF XY:
0.000574
AC XY:
290
AN XY:
505192
show subpopulations
Gnomad4 AFR exome
AF:
0.0217
Gnomad4 AMR exome
AF:
0.00349
Gnomad4 ASJ exome
AF:
0.000947
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000350
Gnomad4 OTH exome
AF:
0.00213
GnomAD4 genome
AF:
0.00656
AC:
993
AN:
151296
Hom.:
8
Cov.:
32
AF XY:
0.00649
AC XY:
480
AN XY:
73940
show subpopulations
Gnomad4 AFR
AF:
0.0219
Gnomad4 AMR
AF:
0.00401
Gnomad4 ASJ
AF:
0.00116
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000103
Gnomad4 OTH
AF:
0.00810
Alfa
AF:
0.0000700
Hom.:
0
Bravo
AF:
0.00805
ExAC
AF:
0.000319
AC:
9

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.080
BayesDel_addAF
Benign
-0.66
T
BayesDel_noAF
Benign
-0.70
CADD
Benign
21
DANN
Benign
0.97
DEOGEN2
Benign
0.016
T;T;T
Eigen
Benign
-0.93
Eigen_PC
Benign
-0.88
FATHMM_MKL
Benign
0.15
N
LIST_S2
Benign
0.27
T;.;.
MetaRNN
Benign
0.0021
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.0
N;N;N
PrimateAI
Pathogenic
0.90
D
PROVEAN
Benign
0.080
N;.;.
REVEL
Benign
0.027
Sift
Benign
0.67
T;.;.
Sift4G
Benign
0.80
T;T;T
Polyphen
0.092
B;B;B
Vest4
0.10
MutPred
0.17
Gain of catalytic residue at A39 (P = 0.1366);Gain of catalytic residue at A39 (P = 0.1366);Gain of catalytic residue at A39 (P = 0.1366);
MVP
0.040
MPC
0.10
ClinPred
0.19
T
GERP RS
1.3
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3
Varity_R
0.035
gMVP
0.15

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.

Other links and lift over

dbSNP: rs542896699; hg19: chr19-50354701; API