Variant 17-59169772-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_018304.4(PRR11):c.20G>A(p.Arg7Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00805 in 1,596,020 control chromosomes in the GnomAD database, including 60 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0063 ( 6 hom., cov: 32)

Exomes 𝑓: 0.0082 ( 54 hom. )

Consequence

PRR11
NM_018304.4 missense

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.530

Variant links:

Genes affected

PRR11 (HGNC:25619): (proline rich 11) Involved in regulation of cell cycle. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Apr 2022]

PRR11 links:

PRR11 (HGNC:):

PRR11 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0053979754).

BP6

Variant 17-59169772-G-A is Benign according to our data. Variant chr17-59169772-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2647972.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRR11	NM_018304.4 linkuse as main transcript	c.20G>A	p.Arg7Gln	missense_variant	2/10	ENST00000262293.9	NP_060774.2	Q96HE9D2SNZ4
PRR11	XM_024450828.2 linkuse as main transcript	c.20G>A	p.Arg7Gln	missense_variant	3/11		XP_024306596.1
PRR11	XM_047436387.1 linkuse as main transcript	c.20G>A	p.Arg7Gln	missense_variant	3/11		XP_047292343.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRR11	ENST00000262293.9 linkuse as main transcript	c.20G>A	p.Arg7Gln	missense_variant	2/10	1	NM_018304.4	ENSP00000262293.5		Q96HE9

Frequencies

GnomAD3 genomes

AF:

0.00627

AC:

952

AN:

151768

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00167

Gnomad AMI

AF:

0.00331

Gnomad AMR

AF:

0.00329

Gnomad ASJ

AF:

0.00606

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.00166

Gnomad FIN

AF:

0.00779

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.00336

GnomAD3 exomes

AF:

0.00609

AC:

1440

AN:

236536

Hom.:

AF XY:

0.00590

AC XY:

756

AN XY:

128122

show subpopulations

Gnomad AFR exome

AF:

0.00163

Gnomad AMR exome

AF:

0.00283

Gnomad ASJ exome

AF:

0.00545

Gnomad EAS exome

AF:

0.000178

Gnomad SAS exome

AF:

0.00147

Gnomad FIN exome

AF:

0.00902

Gnomad NFE exome

AF:

0.00919

Gnomad OTH exome

AF:

0.00601

GnomAD4 exome

AF:

0.00823

AC:

11892

AN:

1444134

Hom.:

Cov.:

AF XY:

0.00810

AC XY:

5818

AN XY:

718124

show subpopulations

Gnomad4 AFR exome

AF:

0.00134

Gnomad4 AMR exome

AF:

0.00299

Gnomad4 ASJ exome

AF:

0.00555

Gnomad4 EAS exome

AF:

0.000101

Gnomad4 SAS exome

AF:

0.00140

Gnomad4 FIN exome

AF:

0.00840

Gnomad4 NFE exome

AF:

0.00962

Gnomad4 OTH exome

AF:

0.00630

GnomAD4 genome

AF:

0.00626

AC:

951

AN:

151886

Hom.:

Cov.:

AF XY:

0.00610

AC XY:

453

AN XY:

74232

show subpopulations

Gnomad4 AFR

AF:

0.00167

Gnomad4 AMR

AF:

0.00322

Gnomad4 ASJ

AF:

0.00606

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.00779

Gnomad4 NFE

AF:

0.0105

Gnomad4 OTH

AF:

0.00332

Alfa

AF:

0.00852

Hom.:

Bravo

AF:

0.00573

TwinsUK

AF:

0.0108

AC:

ALSPAC

AF:

0.00908

AC:

ESP6500AA

AF:

0.00250

AC:

ESP6500EA

AF:

0.00907

AC:

ExAC

AF:

0.00605

AC:

734

Asia WGS

AF:

0.00144

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Apr 01, 2023

PRR11: BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.091

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.42

CADD

Benign

DANN

Benign

0.75

DEOGEN2

Benign

0.029

T;T;.;.;T

Eigen

Benign

-0.65

Eigen_PC

Benign

-0.63

FATHMM_MKL

Benign

0.33

LIST_S2

Benign

0.61

.;T;T;T;T

M_CAP

Benign

0.0012

MetaRNN

Benign

0.0054

T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.2

L;.;.;.;L

PrimateAI

Benign

0.39

PROVEAN

Benign

-1.9

N;.;.;.;.

REVEL

Benign

0.032

Sift

Benign

0.089

T;.;.;.;.

Sift4G

Benign

0.062

T;T;.;D;T

Polyphen

0.086

B;.;.;.;B

Vest4

0.25

MVP

0.52

MPC

0.16

ClinPred

0.0076

GERP RS

1.2

Varity_R

0.041

gMVP

0.10

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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