Variant 11-1889173-C-T 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_001395380.1(PRR33):c.1412G>A(p.Arg471His) variant causes a missense change. The variant allele was found at a frequency of 0.0089 in 673,694 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0080 ( 7 hom., cov: 33)

Exomes 𝑓: 0.0092 ( 35 hom. )

Consequence

PRR33
NM_001395380.1 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 5.89

Variant links:

Genes affected

PRR33 (HGNC:35118): (proline rich 33) Predicted to act upstream of or within response to wounding. [provided by Alliance of Genome Resources, Apr 2022]

PRR33 links:

LSP1 (HGNC:6707): (lymphocyte specific protein 1) This gene encodes an intracellular F-actin binding protein. The protein is expressed in lymphocytes, neutrophils, macrophages, and endothelium and may regulate neutrophil motility, adhesion to fibrinogen matrix proteins, and transendothelial migration. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

LSP1 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=0.006006807).

BP6

Variant 11-1889173-C-T is Benign according to our data. Variant chr11-1889173-C-T is described in ClinVar as [Benign]. Clinvar id is 3024836.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 7 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRR33	NM_001395380.1 linkuse as main transcript	c.1412G>A	p.Arg471His	missense_variant	1/1	ENST00000640310.2	NP_001382309.1
LSP1	NM_002339.3 linkuse as main transcript	c.*13+1597C>T		intron_variant		ENST00000311604.8	NP_002330.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRR33	ENST00000640310.2 linkuse as main transcript	c.1412G>A	p.Arg471His	missense_variant	1/1		NM_001395380.1	ENSP00000491327	P1
LSP1	ENST00000311604.8 linkuse as main transcript	c.*13+1597C>T		intron_variant		1	NM_002339.3	ENSP00000308383	P2	P33241-1

Frequencies

GnomAD3 genomes

AF:

0.00796

AC:

1212

AN:

152248

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00195

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.0446

Gnomad EAS

AF:

0.00115

Gnomad SAS

AF:

0.000827

Gnomad FIN

AF:

0.00884

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0119

Gnomad OTH

AF:

0.00573

GnomAD3 exomes

AF:

0.00749

AC:

860

AN:

114842

Hom.:

AF XY:

0.00720

AC XY:

443

AN XY:

61488

show subpopulations

Gnomad AFR exome

AF:

0.00142

Gnomad AMR exome

AF:

0.00350

Gnomad ASJ exome

AF:

0.0405

Gnomad EAS exome

AF:

0.000868

Gnomad SAS exome

AF:

0.00111

Gnomad FIN exome

AF:

0.00851

Gnomad NFE exome

AF:

0.00972

Gnomad OTH exome

AF:

0.00664

GnomAD4 exome

AF:

0.00917

AC:

4781

AN:

521328

Hom.:

Cov.:

AF XY:

0.00882

AC XY:

2462

AN XY:

279124

show subpopulations

Gnomad4 AFR exome

AF:

0.00222

Gnomad4 AMR exome

AF:

0.00338

Gnomad4 ASJ exome

AF:

0.0426

Gnomad4 EAS exome

AF:

0.000292

Gnomad4 SAS exome

AF:

0.000907

Gnomad4 FIN exome

AF:

0.00854

Gnomad4 NFE exome

AF:

0.0108

Gnomad4 OTH exome

AF:

0.00994

GnomAD4 genome

AF:

0.00795

AC:

1212

AN:

152366

Hom.:

Cov.:

AF XY:

0.00776

AC XY:

578

AN XY:

74510

show subpopulations

Gnomad4 AFR

AF:

0.00195

Gnomad4 AMR

AF:

0.00287

Gnomad4 ASJ

AF:

0.0446

Gnomad4 EAS

AF:

0.00116

Gnomad4 SAS

AF:

0.000827

Gnomad4 FIN

AF:

0.00884

Gnomad4 NFE

AF:

0.0120

Gnomad4 OTH

AF:

0.00567

Alfa

AF:

0.0118

Hom.:

Bravo

AF:

0.00729

TwinsUK

AF:

0.0119

AC:

ALSPAC

AF:

0.0114

AC:

ExAC

AF:

0.00559

AC:

119

Asia WGS

AF:

0.000866

AC:

AN:

3478

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

CeGaT Center for Human Genetics Tuebingen

Feb 01, 2024

PRR33: BP4, BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.31

BayesDel_noAF

Benign

-0.21

CADD

Pathogenic

DANN

Pathogenic

1.0

Eigen

Uncertain

0.22

Eigen_PC

Uncertain

0.23

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.67

MetaRNN

Benign

0.0060

MetaSVM

Uncertain

-0.22

MutationTaster

Benign

1.0

D;D;D;D

ClinPred

0.028

GERP RS

3.7

gMVP

0.093

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