GeneBe

rs34990810

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_015629.4(PRPF31):​c.1074-50C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000712 in 1,405,282 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 7.1e-7 ( 0 hom. )

Consequence

PRPF31
NM_015629.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.22

Publications

0 publications found
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 Gene-Disease associations (from GenCC):
  • PRPF31-related retinopathy
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • retinitis pigmentosa 11
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
  • retinitis pigmentosa
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PRPF31NM_015629.4 linkc.1074-50C>A intron_variant Intron 10 of 13 ENST00000321030.9 NP_056444.3
PRPF31XM_006723137.5 linkc.1074-50C>A intron_variant Intron 10 of 13 XP_006723200.1
PRPF31XM_047438587.1 linkc.*160C>A downstream_gene_variant XP_047294543.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRPF31ENST00000321030.9 linkc.1074-50C>A intron_variant Intron 10 of 13 1 NM_015629.4 ENSP00000324122.4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
7.12e-7
AC:
1
AN:
1405282
Hom.:
0
Cov.:
64
AF XY:
0.00
AC XY:
0
AN XY:
693426
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
32712
American (AMR)
AF:
0.00
AC:
0
AN:
35790
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
25150
East Asian (EAS)
AF:
0.00
AC:
0
AN:
37696
South Asian (SAS)
AF:
0.00
AC:
0
AN:
79956
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
48182
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
4234
European-Non Finnish (NFE)
AF:
9.23e-7
AC:
1
AN:
1083346
Other (OTH)
AF:
0.00
AC:
0
AN:
58216
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.15
DANN
Benign
0.85
PhyloP100
-1.2
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.3

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

Other links and lift over

dbSNP: rs34990810; hg19: chr19-54631630; API