Variant chr19-49594527-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

The NM_020719.3(PRR12):c.273T>C(p.Leu91Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.262 in 1,612,888 control chromosomes in the GnomAD database, including 61,013 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.33 ( 9461 hom., cov: 31)

Exomes 𝑓: 0.26 ( 51552 hom. )

Consequence

PRR12
NM_020719.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.889

Variant links:

Genes affected

PRR12 (HGNC:29217): (proline rich 12) This gene encodes a proline-rich protein that contains two A-T hook DNA binding domains. A chromosomal translocation and gene fusion between this gene and zinc finger, MIZ-type containing 1 (Gene ID: 57178) may underlie intellectual disability and neuropsychiatric problems in a human patient. Enriched expression of this gene in embryonic mouse brain suggests that this gene may play a role in nervous system development. [provided by RefSeq, Jul 2016]

PRR12 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 19-49594527-T-C is Benign according to our data. Variant chr19-49594527-T-C is described in ClinVar as [Benign]. Clinvar id is 3060389.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.889 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRR12	NM_020719.3 linkuse as main transcript	c.273T>C	p.Leu91Leu	synonymous_variant	3/14	ENST00000418929.7	NP_065770.1	Q9ULL5-3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRR12	ENST00000418929.7 linkuse as main transcript	c.273T>C	p.Leu91Leu	synonymous_variant	3/14	5	NM_020719.3	ENSP00000394510.1		Q9ULL5-3

Frequencies

GnomAD3 genomes

AF:

0.329

AC:

49935

AN:

151760

Hom.:

9437

Cov.:

show subpopulations

Gnomad AFR

AF:

0.518

Gnomad AMI

AF:

0.243

Gnomad AMR

AF:

0.294

Gnomad ASJ

AF:

0.242

Gnomad EAS

AF:

0.202

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.206

Gnomad MID

AF:

0.342

Gnomad NFE

AF:

0.249

Gnomad OTH

AF:

0.321

GnomAD3 exomes

AF:

0.290

AC:

71933

AN:

248238

Hom.:

11553

AF XY:

0.292

AC XY:

39416

AN XY:

134858

show subpopulations

Gnomad AFR exome

AF:

0.520

Gnomad AMR exome

AF:

0.302

Gnomad ASJ exome

AF:

0.243

Gnomad EAS exome

AF:

0.199

Gnomad SAS exome

AF:

0.436

Gnomad FIN exome

AF:

0.216

Gnomad NFE exome

AF:

0.249

Gnomad OTH exome

AF:

0.273

GnomAD4 exome

AF:

0.255

AC:

373235

AN:

1461010

Hom.:

51552

Cov.:

AF XY:

0.260

AC XY:

189298

AN XY:

726800

show subpopulations

Gnomad4 AFR exome

AF:

0.520

Gnomad4 AMR exome

AF:

0.300

Gnomad4 ASJ exome

AF:

0.247

Gnomad4 EAS exome

AF:

0.177

Gnomad4 SAS exome

AF:

0.431

Gnomad4 FIN exome

AF:

0.215

Gnomad4 NFE exome

AF:

0.236

Gnomad4 OTH exome

AF:

0.270

GnomAD4 genome

AF:

0.329

AC:

50012

AN:

151878

Hom.:

9461

Cov.:

AF XY:

0.327

AC XY:

24246

AN XY:

74236

show subpopulations

Gnomad4 AFR

AF:

0.519

Gnomad4 AMR

AF:

0.294

Gnomad4 ASJ

AF:

0.242

Gnomad4 EAS

AF:

0.201

Gnomad4 SAS

AF:

0.441

Gnomad4 FIN

AF:

0.206

Gnomad4 NFE

AF:

0.249

Gnomad4 OTH

AF:

0.323

Alfa

AF:

0.281

Hom.:

4100

Bravo

AF:

0.340

Asia WGS

AF:

0.351

AC:

1218

AN:

3478

EpiCase

AF:

0.257

EpiControl

AF:

0.249

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PRR12-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 21, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

DANN

Benign

0.77

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