9-113275672-C-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2

The NM_001244926.2(PRPF4):​c.-72C>T variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 1,550,452 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0011 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 1 hom. )

Consequence

PRPF4
NM_001244926.2 5_prime_UTR_premature_start_codon_gain

Scores

2

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.30
Variant links:
Genes affected
PRPF4 (HGNC:17349): (pre-mRNA splicing tri-snRNP complex factor PRPF4) The protein encoded by this gene is part of a heteromeric complex that binds U4, U5, and U6 small nuclear RNAs and is involved in pre-mRNA splicing. The encoded protein also is a mitotic checkpoint protein and a regulator of chemoresistance in human ovarian cancer. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2016]
CDC26 (HGNC:17839): (cell division cycle 26) The protein encoded by this gene is highly similar to Saccharomyces cerevisiae Cdc26, a component of cell cycle anaphase-promoting complex (APC). APC is composed of a group of highly conserved proteins and functions as a cell cycle-regulated ubiquitin-protein ligase. APC thus is responsible for the cell cycle regulated proteolysis of various proteins. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -7 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
Variant 9-113275672-C-T is Benign according to our data. Variant chr9-113275672-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3042380.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
High AC in GnomAd4 at 166 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PRPF4NM_001244926.2 linkc.-72C>T 5_prime_UTR_premature_start_codon_gain_variant Exon 1 of 14 ENST00000374198.5 NP_001231855.1 O43172-2Q5T1M7
PRPF4NM_001244926.2 linkc.-72C>T 5_prime_UTR_variant Exon 1 of 14 ENST00000374198.5 NP_001231855.1 O43172-2Q5T1M7
CDC26NM_139286.4 linkc.-442G>A upstream_gene_variant ENST00000374206.4 NP_644815.1 Q8NHZ8A0A024R832

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PRPF4ENST00000374198 linkc.-72C>T 5_prime_UTR_premature_start_codon_gain_variant Exon 1 of 14 1 NM_001244926.2 ENSP00000363313.4 O43172-2
PRPF4ENST00000374198 linkc.-72C>T 5_prime_UTR_variant Exon 1 of 14 1 NM_001244926.2 ENSP00000363313.4 O43172-2
CDC26ENST00000374206.4 linkc.-442G>A upstream_gene_variant 1 NM_139286.4 ENSP00000363322.3 Q8NHZ8

Frequencies

GnomAD3 genomes
AF:
0.00109
AC:
166
AN:
152206
Hom.:
1
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00209
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00179
Gnomad OTH
AF:
0.00239
GnomAD4 exome
AF:
0.00166
AC:
2322
AN:
1398128
Hom.:
1
Cov.:
26
AF XY:
0.00154
AC XY:
1068
AN XY:
692342
show subpopulations
Gnomad4 AFR exome
AF:
0.000319
Gnomad4 AMR exome
AF:
0.00160
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000373
Gnomad4 FIN exome
AF:
0.0000403
Gnomad4 NFE exome
AF:
0.00198
Gnomad4 OTH exome
AF:
0.00203
GnomAD4 genome
AF:
0.00109
AC:
166
AN:
152324
Hom.:
1
Cov.:
32
AF XY:
0.000993
AC XY:
74
AN XY:
74492
show subpopulations
Gnomad4 AFR
AF:
0.000168
Gnomad4 AMR
AF:
0.00209
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00179
Gnomad4 OTH
AF:
0.00236
Bravo
AF:
0.00121

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

PRPF4-related disorder Benign:1
Apr 02, 2019
PreventionGenetics, part of Exact Sciences
Significance: Likely benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.42
CADD
Benign
11
DANN
Benign
0.87

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.

Other links and lift over

dbSNP: rs377499486; hg19: chr9-116037952; COSMIC: COSV104684050; COSMIC: COSV104684050; API