rs767595091
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_025065.7(RPF1):c.73C>T(p.Leu25Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_025065.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RPF1 | ENST00000370654.6 | c.73C>T | p.Leu25Phe | missense_variant | Exon 1 of 9 | 1 | NM_025065.7 | ENSP00000359688.5 | ||
RPF1 | ENST00000370656.5 | c.73C>T | p.Leu25Phe | missense_variant | Exon 1 of 3 | 2 | ENSP00000359690.1 | |||
ENSG00000285361 | ENST00000644783.1 | n.*197C>T | downstream_gene_variant |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250338Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135508
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461480Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727026
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.73C>T (p.L25F) alteration is located in exon 1 (coding exon 1) of the RPF1 gene. This alteration results from a C to T substitution at nucleotide position 73, causing the leucine (L) at amino acid position 25 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at