Variant 19-54126322-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_015629.4(PRPF31):c.856-206T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,098 control chromosomes in the GnomAD database, including 2,556 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 0.18 ( 2556 hom., cov: 33)

Consequence

PRPF31
NM_015629.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.803

Variant links:

Genes affected

PRPF31 (HGNC:15446): (pre-mRNA processing factor 31) This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]

PRPF31 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.234 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
PRPF31	NM_015629.4 link	c.856-206T>C	intron_variant	ENST00000321030.9	NP_056444.3	Q8WWY3-1
PRPF31	XM_006723137.5 link	c.856-206T>C	intron_variant		XP_006723200.1	Q8WWY3-1
PRPF31	XM_047438587.1 link	c.856-178T>C	intron_variant		XP_047294543.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRPF31	ENST00000321030.9 link	c.856-206T>C		intron_variant		1	NM_015629.4	ENSP00000324122.4		Q8WWY3-1

Frequencies

GnomAD3 genomes

AF:

0.175

AC:

26637

AN:

151978

Hom.:

2552

Cov.:

show subpopulations

Gnomad AFR

AF:

0.124

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.135

Gnomad ASJ

AF:

0.145

Gnomad EAS

AF:

0.246

Gnomad SAS

AF:

0.195

Gnomad FIN

AF:

0.262

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.199

Gnomad OTH

AF:

0.152

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.175

AC:

26655

AN:

152098

Hom.:

2556

Cov.:

AF XY:

0.175

AC XY:

13038

AN XY:

74332

show subpopulations

Gnomad4 AFR

AF:

0.123

Gnomad4 AMR

AF:

0.135

Gnomad4 ASJ

AF:

0.145

Gnomad4 EAS

AF:

0.245

Gnomad4 SAS

AF:

0.194

Gnomad4 FIN

AF:

0.262

Gnomad4 NFE

AF:

0.199

Gnomad4 OTH

AF:

0.156

Alfa

AF:

0.179

Hom.:

3254

Bravo

AF:

0.161

Asia WGS

AF:

0.257

AC:

896

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.24

DANN

Benign

0.34

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