rs7679
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_022104.4(PCIF1):c.*108T>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 0.17 in 1,533,340 control chromosomes in the GnomAD database, including 23,743 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 0.13 ( 1626 hom., cov: 32)
Exomes 𝑓: 0.17 ( 22117 hom. )
Consequence
PCIF1
NM_022104.4 3_prime_UTR
NM_022104.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0350
Genes affected
PCIF1 (HGNC:16200): (phosphorylated CTD interacting factor 1) Enables RNA polymerase II C-terminal domain phosphoserine binding activity; S-adenosyl-L-methionine binding activity; and mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity. Involved in mRNA methylation; negative regulation of translation; and positive regulation of translation. Located in intercellular bridge; microtubule cytoskeleton; and nucleoplasm. [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=-0.83).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.194 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PCIF1 | NM_022104.4 | c.*108T>C | 3_prime_UTR_variant | 17/17 | ENST00000372409.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PCIF1 | ENST00000372409.8 | c.*108T>C | 3_prime_UTR_variant | 17/17 | 1 | NM_022104.4 | P1 | ||
PCIF1 | ENST00000479348.2 | c.*250T>C | 3_prime_UTR_variant | 6/6 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.130 AC: 19801AN: 151874Hom.: 1626 Cov.: 32
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GnomAD4 exome AF: 0.175 AC: 241103AN: 1381348Hom.: 22117 Cov.: 33 AF XY: 0.176 AC XY: 120081AN XY: 683282
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GnomAD4 genome ? AF: 0.130 AC: 19800AN: 151992Hom.: 1626 Cov.: 32 AF XY: 0.130 AC XY: 9690AN XY: 74300
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at