Variant 10-133347446-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_145202.5(PRAP1):c.8+21C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.8 in 1,606,498 control chromosomes in the GnomAD database, including 519,785 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.72 ( 40761 hom., cov: 34)

Exomes 𝑓: 0.81 ( 479024 hom. )

Consequence

PRAP1
NM_145202.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.275

Variant links:

Genes affected

PRAP1 (HGNC:23304): (proline rich acidic protein 1) Predicted to enable triglyceride binding activity. Involved in DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest; deactivation of mitotic spindle assembly checkpoint; and negative regulation of apoptotic process. Predicted to be located in endoplasmic reticulum and extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

PRAP1 links:

ZNF511-PRAP1 (HGNC:38088): (ZNF511-PRAP1 readthrough) This locus represents naturally occurring readthrough transcription between the neighboring ZNF511 (zinc finger protein 511) and PRAP1 (proline-rich acidic protein 1) genes on chromosome 10. The putative readthrough transcript may encode a fusion protein that shares sequence identity with each individual gene product and may be involved in the regulation of gene promoters, particularly those found on transfected plasmids. [provided by RefSeq, Apr 2017]

ZNF511-PRAP1 links:

ENSG00000226699 (HGNC:):

ENSG00000226699 links:

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 (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
PRAP1	NM_145202.5 linkuse as main transcript	c.8+21C>T	intron_variant	ENST00000433452.6	NP_660203.3	Q96NZ9-1
ZNF511-PRAP1	NM_001396060.1 linkuse as main transcript	c.681-2649C>T	intron_variant		NP_001382989.1
PRAP1	NM_001145201.2 linkuse as main transcript	c.8+21C>T	intron_variant		NP_001138673.1	Q96NZ9-4A6XND8

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
PRAP1	ENST00000433452.6 linkuse as main transcript	c.8+21C>T	intron_variant	1	NM_145202.5	ENSP00000416126.2	Q96NZ9-1
ZNF511-PRAP1	ENST00000368554.8 linkuse as main transcript	c.507-2649C>T	intron_variant	2		ENSP00000357542.5	H7BY64
PRAP1	ENST00000463201.2 linkuse as main transcript	c.8+21C>T	intron_variant	1		ENSP00000486265.1	Q96NZ9-4
ENSG00000226699	ENST00000452591.1 linkuse as main transcript	n.141-1649G>A	intron_variant	5

Frequencies

GnomAD3 genomes

AF:

0.715

AC:

108771

AN:

152046

Hom.:

40744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.473

Gnomad AMI

AF:

0.619

Gnomad AMR

AF:

0.732

Gnomad ASJ

AF:

0.820

Gnomad EAS

AF:

0.927

Gnomad SAS

AF:

0.810

Gnomad FIN

AF:

0.847

Gnomad MID

AF:

0.709

Gnomad NFE

AF:

0.811

Gnomad OTH

AF:

0.729

GnomAD3 exomes

AF:

0.795

AC:

193048

AN:

242732

Hom.:

78023

AF XY:

0.803

AC XY:

105439

AN XY:

131358

show subpopulations

Gnomad AFR exome

AF:

0.465

Gnomad AMR exome

AF:

0.745

Gnomad ASJ exome

AF:

0.823

Gnomad EAS exome

AF:

0.939

Gnomad SAS exome

AF:

0.816

Gnomad FIN exome

AF:

0.851

Gnomad NFE exome

AF:

0.816

Gnomad OTH exome

AF:

0.806

GnomAD4 exome

AF:

0.809

AC:

1176897

AN:

1454334

Hom.:

479024

Cov.:

AF XY:

0.811

AC XY:

586256

AN XY:

723282

show subpopulations

Gnomad4 AFR exome

AF:

0.467

Gnomad4 AMR exome

AF:

0.742

Gnomad4 ASJ exome

AF:

0.830

Gnomad4 EAS exome

AF:

0.908

Gnomad4 SAS exome

AF:

0.819

Gnomad4 FIN exome

AF:

0.850

Gnomad4 NFE exome

AF:

0.817

Gnomad4 OTH exome

AF:

0.791

GnomAD4 genome

AF:

0.715

AC:

108818

AN:

152164

Hom.:

40761

Cov.:

AF XY:

0.720

AC XY:

53571

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.473

Gnomad4 AMR

AF:

0.732

Gnomad4 ASJ

AF:

0.820

Gnomad4 EAS

AF:

0.928

Gnomad4 SAS

AF:

0.810

Gnomad4 FIN

AF:

0.847

Gnomad4 NFE

AF:

0.811

Gnomad4 OTH

AF:

0.732

Alfa

AF:

0.758

Hom.:

8859

Bravo

AF:

0.696

Asia WGS

AF:

0.833

AC:

2899

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

9.2

DANN

Benign

0.82

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over