Variant rs11205362 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004698.4(PRPF3):c.146-17G>A variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 1,609,420 control chromosomes in the GnomAD database, including 9,760 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.082 ( 678 hom., cov: 32)

Exomes 𝑓: 0.11 ( 9082 hom. )

Consequence

PRPF3
NM_004698.4 splice_polypyrimidine_tract, intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.404

Variant links:

Genes affected

PRPF3 (HGNC:17348): (pre-mRNA processing factor 3) The removal of introns from nuclear pre-mRNAs occurs on complexes called spliceosomes, which are made up of 4 small nuclear ribonucleoprotein (snRNP) particles and an undefined number of transiently associated splicing factors. This gene product is one of several proteins that associate with U4 and U6 snRNPs. Mutations in this gene are associated with retinitis pigmentosa-18. [provided by RefSeq, Jul 2008]

PRPF3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 1-150325734-G-A is Benign according to our data. Variant chr1-150325734-G-A is described in ClinVar as [Benign]. Clinvar id is 1165123.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRPF3	NM_004698.4 linkuse as main transcript	c.146-17G>A		splice_polypyrimidine_tract_variant, intron_variant		ENST00000324862.7	NP_004689.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRPF3	ENST00000324862.7 linkuse as main transcript	c.146-17G>A		splice_polypyrimidine_tract_variant, intron_variant		1	NM_004698.4	ENSP00000315379	P1	O43395-1
PRPF3	ENST00000496202.5 linkuse as main transcript	n.308-17G>A		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes

AF:

0.0819

AC:

12449

AN:

151974

Hom.:

678

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0208

Gnomad AMI

AF:

0.0703

Gnomad AMR

AF:

0.0676

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0288

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.0675

GnomAD3 exomes

AF:

0.0839

AC:

21101

AN:

251456

Hom.:

1166

AF XY:

0.0842

AC XY:

11444

AN XY:

135910

show subpopulations

Gnomad AFR exome

AF:

0.0183

Gnomad AMR exome

AF:

0.0454

Gnomad ASJ exome

AF:

0.0922

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0327

Gnomad FIN exome

AF:

0.153

Gnomad NFE exome

AF:

0.118

Gnomad OTH exome

AF:

0.0963

GnomAD4 exome

AF:

0.106

AC:

154364

AN:

1457328

Hom.:

9082

Cov.:

AF XY:

0.104

AC XY:

75563

AN XY:

725126

show subpopulations

Gnomad4 AFR exome

AF:

0.0175

Gnomad4 AMR exome

AF:

0.0478

Gnomad4 ASJ exome

AF:

0.0976

Gnomad4 EAS exome

AF:

0.0000506

Gnomad4 SAS exome

AF:

0.0327

Gnomad4 FIN exome

AF:

0.144

Gnomad4 NFE exome

AF:

0.119

Gnomad4 OTH exome

AF:

0.0990

GnomAD4 genome

AF:

0.0818

AC:

12445

AN:

152092

Hom.:

678

Cov.:

AF XY:

0.0810

AC XY:

6026

AN XY:

74356

show subpopulations

Gnomad4 AFR

AF:

0.0207

Gnomad4 AMR

AF:

0.0675

Gnomad4 ASJ

AF:

0.0963

Gnomad4 EAS

AF:

0.000772

Gnomad4 SAS

AF:

0.0293

Gnomad4 FIN

AF:

0.155

Gnomad4 NFE

AF:

0.121

Gnomad4 OTH

AF:

0.0668

Alfa

AF:

0.110

Hom.:

763

Bravo

AF:

0.0726

Asia WGS

AF:

0.0180

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	May 15, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

DANN

Benign

0.53

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