rs7943546
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001286581.2(PHRF1):c.*371T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.234 in 330,664 control chromosomes in the GnomAD database, including 10,599 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 0.27 ( 6323 hom., cov: 33)
Exomes 𝑓: 0.20 ( 4276 hom. )
Consequence
PHRF1
NM_001286581.2 3_prime_UTR
NM_001286581.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.532
Genes affected
PHRF1 (HGNC:24351): (PHD and ring finger domains 1) Predicted to enable RNA polymerase binding activity. Predicted to be involved in mRNA processing and transcription by RNA polymerase II. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.95).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHRF1 | NM_001286581.2 | c.*371T>C | 3_prime_UTR_variant | 18/18 | ENST00000264555.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHRF1 | ENST00000264555.10 | c.*371T>C | 3_prime_UTR_variant | 18/18 | 1 | NM_001286581.2 | P5 |
Frequencies
GnomAD3 genomes ? AF: 0.268 AC: 40697AN: 152138Hom.: 6316 Cov.: 33
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GnomAD4 exome AF: 0.205 AC: 36500AN: 178408Hom.: 4276 Cov.: 0 AF XY: 0.200 AC XY: 18340AN XY: 91870
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GnomAD4 genome ? AF: 0.268 AC: 40734AN: 152256Hom.: 6323 Cov.: 33 AF XY: 0.258 AC XY: 19180AN XY: 74454
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at