Variant 11-36401129-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_001160167.2(PRR5L):c.8G>A(p.Arg3His) variant causes a missense change. The variant allele was found at a frequency of 0.00283 in 1,614,078 control chromosomes in the GnomAD database, including 126 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.015 ( 73 hom., cov: 33)

Exomes 𝑓: 0.0015 ( 53 hom. )

Consequence

PRR5L
NM_001160167.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.88

Variant links:

Genes affected

PRR5L (HGNC:25878): (proline rich 5 like) Enables ubiquitin protein ligase binding activity. Involved in several processes, including TORC2 signaling; positive regulation of mRNA catabolic process; and regulation of fibroblast migration. Part of TORC2 complex. [provided by Alliance of Genome Resources, Apr 2022]

PRR5L links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0029927492).

BP6

Variant 11-36401129-G-A is Benign according to our data. Variant chr11-36401129-G-A is described in ClinVar as [Benign]. Clinvar id is 776603.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
PRR5L	NM_001160167.2 linkuse as main transcript	c.8G>A	p.Arg3His	missense_variant	2/9	ENST00000530639.6
PRR5L	NM_024841.5 linkuse as main transcript	c.8G>A	p.Arg3His	missense_variant	3/10
PRR5L	NM_001160169.1 linkuse as main transcript	c.8G>A	p.Arg3His	missense_variant	1/7
PRR5L	NM_001160168.2 linkuse as main transcript	c.3-18126G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRR5L	ENST00000530639.6 linkuse as main transcript	c.8G>A	p.Arg3His	missense_variant	2/9	2	NM_001160167.2	P1	Q6MZQ0-1

Frequencies

GnomAD3 genomes

AF:

0.0153

AC:

2333

AN:

152182

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0537

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00543

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.000118

Gnomad OTH

AF:

0.00813

GnomAD3 exomes

AF:

0.00415

AC:

1040

AN:

250860

Hom.:

AF XY:

0.00305

AC XY:

413

AN XY:

135552

show subpopulations

Gnomad AFR exome

AF:

0.0568

Gnomad AMR exome

AF:

0.00272

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000971

Gnomad OTH exome

AF:

0.00196

GnomAD4 exome

AF:

0.00153

AC:

2238

AN:

1461778

Hom.:

Cov.:

AF XY:

0.00130

AC XY:

945

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.0546

Gnomad4 AMR exome

AF:

0.00297

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000464

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000800

Gnomad4 OTH exome

AF:

0.00280

GnomAD4 genome

AF:

0.0153

AC:

2333

AN:

152300

Hom.:

Cov.:

AF XY:

0.0144

AC XY:

1069

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0535

Gnomad4 AMR

AF:

0.00543

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000118

Gnomad4 OTH

AF:

0.00805

Alfa

AF:

0.00308

Hom.:

Bravo

AF:

0.0181

ESP6500AA

AF:

0.0574

AC:

253

ESP6500EA

AF:

0.000116

AC:

ExAC

AF:

0.00497

AC:

603

Asia WGS

AF:

0.00231

AC:

AN:

3478

EpiCase

AF:

0.000164

EpiControl

AF:

0.000178

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Dec 20, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.49

BayesDel_noAF

Benign

-0.44

Cadd

Uncertain

Dann

Pathogenic

1.0

DEOGEN2

Benign

0.0053

T;.;.;T;T;.;T;.;T;T;.

Eigen

Uncertain

0.41

Eigen_PC

Uncertain

0.46

FATHMM_MKL

Pathogenic

0.99

MetaRNN

Benign

0.0030

T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.81

L;.;.;.;L;.;.;.;.;.;L

MutationTaster

Benign

0.96

D;D;D;D

PrimateAI

Uncertain

0.60

PROVEAN

Benign

-0.050

N;N;N;N;N;N;N;N;N;N;N

REVEL

Benign

0.12

Sift

Benign

0.034

D;D;D;D;D;D;D;D;D;D;D

Sift4G

Benign

0.16

T;T;T;T;T;T;T;T;T;T;T

Polyphen

0.99

D;.;.;.;D;.;.;.;.;.;.

Vest4

0.34

MVP

0.38

MPC

0.78

ClinPred

0.019

GERP RS

5.2

Varity_R

0.092

gMVP

0.33

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over