rs486907
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_021133.4(RNASEL):c.1385G>A(p.Arg462Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.335 in 1,613,854 control chromosomes in the GnomAD database, including 94,567 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_021133.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNASEL | NM_021133.4 | c.1385G>A | p.Arg462Gln | missense_variant | 2/7 | ENST00000367559.7 | |
RNASEL | XM_047427096.1 | c.1385G>A | p.Arg462Gln | missense_variant | 2/7 | ||
RNASEL | XM_047427106.1 | c.1385G>A | p.Arg462Gln | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNASEL | ENST00000367559.7 | c.1385G>A | p.Arg462Gln | missense_variant | 2/7 | 1 | NM_021133.4 | P1 | |
RNASEL | ENST00000539397.1 | c.1385G>A | p.Arg462Gln | missense_variant | 2/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.282 AC: 42890AN: 151884Hom.: 6974 Cov.: 32
GnomAD3 exomes AF: 0.305 AC: 76756AN: 251298Hom.: 12737 AF XY: 0.315 AC XY: 42765AN XY: 135806
GnomAD4 exome AF: 0.340 AC: 497143AN: 1461852Hom.: 87596 Cov.: 45 AF XY: 0.340 AC XY: 247265AN XY: 727232
GnomAD4 genome ? AF: 0.282 AC: 42892AN: 152002Hom.: 6971 Cov.: 32 AF XY: 0.282 AC XY: 20959AN XY: 74290
ClinVar
Submissions by phenotype
Prostate cancer, hereditary, 1 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Laboratory of Virology, Oncology, Biosciences and Environment, Faculty of Sciences and Techniques, Mohammedia- University Hassan II of Casablanca | Aug 17, 2022 | - - |
Hereditary cancer Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | Jan 23, 2024 | - - |
RECLASSIFIED - CDH1 POLYMORPHISM Other:1
risk factor, no assertion criteria provided | literature only | OMIM | Dec 01, 2002 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at