Variant 6-30562719-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_025263.4(PRR3):c.*224T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 417,860 control chromosomes in the GnomAD database, including 105,665 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 0.73 ( 40932 hom., cov: 33)

Exomes 𝑓: 0.69 ( 64733 hom. )

Consequence

PRR3
NM_025263.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.59

Variant links:

Genes affected

PRR3 (HGNC:21149): (proline rich 3) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

PRR3 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRR3	NM_025263.4 linkuse as main transcript	c.*224T>C		3_prime_UTR_variant	4/4	ENST00000376560.8
PRR3	NM_001077497.3 linkuse as main transcript	c.*224T>C		3_prime_UTR_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRR3	ENST00000376560.8 linkuse as main transcript	c.*224T>C		3_prime_UTR_variant	4/4	1	NM_025263.4	P2	P79522-1

Frequencies

GnomAD3 genomes

AF:

0.730

AC:

110949

AN:

152088

Hom.:

40885

Cov.:

show subpopulations

Gnomad AFR

AF:

0.840

Gnomad AMI

AF:

0.752

Gnomad AMR

AF:

0.652

Gnomad ASJ

AF:

0.832

Gnomad EAS

AF:

0.697

Gnomad SAS

AF:

0.828

Gnomad FIN

AF:

0.680

Gnomad MID

AF:

0.791

Gnomad NFE

AF:

0.677

Gnomad OTH

AF:

0.727

GnomAD4 exome

AF:

0.694

AC:

184375

AN:

265652

Hom.:

64733

Cov.:

AF XY:

0.696

AC XY:

95052

AN XY:

136580

show subpopulations

Gnomad4 AFR exome

AF:

0.841

Gnomad4 AMR exome

AF:

0.653

Gnomad4 ASJ exome

AF:

0.824

Gnomad4 EAS exome

AF:

0.723

Gnomad4 SAS exome

AF:

0.779

Gnomad4 FIN exome

AF:

0.672

Gnomad4 NFE exome

AF:

0.673

Gnomad4 OTH exome

AF:

0.718

GnomAD4 genome

AF:

0.730

AC:

111055

AN:

152208

Hom.:

40932

Cov.:

AF XY:

0.727

AC XY:

54068

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.840

Gnomad4 AMR

AF:

0.652

Gnomad4 ASJ

AF:

0.832

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.829

Gnomad4 FIN

AF:

0.680

Gnomad4 NFE

AF:

0.677

Gnomad4 OTH

AF:

0.730

Alfa

AF:

0.696

Hom.:

51398

Bravo

AF:

0.732

Asia WGS

AF:

0.784

AC:

2728

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.92

DANN

Benign

0.17

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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