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
Consequence
NM_001244926.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRPF4 | NM_001244926.2 | c.-72C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 14 | ENST00000374198.5 | NP_001231855.1 | ||
PRPF4 | NM_001244926.2 | c.-72C>T | 5_prime_UTR_variant | Exon 1 of 14 | ENST00000374198.5 | NP_001231855.1 | ||
CDC26 | NM_139286.4 | c.-442G>A | upstream_gene_variant | ENST00000374206.4 | NP_644815.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRPF4 | ENST00000374198 | c.-72C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 1 of 14 | 1 | NM_001244926.2 | ENSP00000363313.4 | |||
PRPF4 | ENST00000374198 | c.-72C>T | 5_prime_UTR_variant | Exon 1 of 14 | 1 | NM_001244926.2 | ENSP00000363313.4 | |||
CDC26 | ENST00000374206.4 | c.-442G>A | upstream_gene_variant | 1 | NM_139286.4 | ENSP00000363322.3 |
Frequencies
GnomAD3 genomes AF: 0.00109 AC: 166AN: 152206Hom.: 1 Cov.: 32
GnomAD4 exome AF: 0.00166 AC: 2322AN: 1398128Hom.: 1 Cov.: 26 AF XY: 0.00154 AC XY: 1068AN XY: 692342
GnomAD4 genome AF: 0.00109 AC: 166AN: 152324Hom.: 1 Cov.: 32 AF XY: 0.000993 AC XY: 74AN XY: 74492
ClinVar
Submissions by phenotype
PRPF4-related disorder Benign:1
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:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at