rs13053624
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000354373.2(RFPL1):c.*92A>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 892,150 control chromosomes in the GnomAD database, including 13,485 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 0.17 ( 2237 hom., cov: 32)
Exomes 𝑓: 0.17 ( 11248 hom. )
Consequence
RFPL1
ENST00000354373.2 3_prime_UTR
ENST00000354373.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.733
Genes affected
RFPL1 (HGNC:9977): (ret finger protein like 1) Predicted to enable ubiquitin-protein transferase activity. Involved in several processes, including negative regulation of G2/M transition of mitotic cell cycle; negative regulation of cell division; and positive regulation of proteolysis. Located in cytoplasm. [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=-0.93).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RFPL1 | NM_021026.2 | c.*92A>T | 3_prime_UTR_variant | 2/2 | ENST00000354373.2 | ||
RFPL1 | NM_001393612.1 | c.*92A>T | 3_prime_UTR_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RFPL1 | ENST00000354373.2 | c.*92A>T | 3_prime_UTR_variant | 2/2 | 1 | NM_021026.2 | P1 | ||
RFPL1S | ENST00000461286.4 | n.308-85T>A | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25232AN: 152020Hom.: 2231 Cov.: 32
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GnomAD4 exome AF: 0.168 AC: 124621AN: 740012Hom.: 11248 Cov.: 10 AF XY: 0.166 AC XY: 61542AN XY: 371052
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GnomAD4 genome ? AF: 0.166 AC: 25273AN: 152138Hom.: 2237 Cov.: 32 AF XY: 0.160 AC XY: 11927AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at