rs121908688
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_003579.4(RAD54L):c.188C>A(p.Pro63His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,461,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P63A) has been classified as Uncertain significance.
Frequency
Consequence
NM_003579.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD54L | NM_003579.4 | c.188C>A | p.Pro63His | missense_variant | 3/18 | ENST00000371975.9 | |
RAD54L | NM_001142548.2 | c.188C>A | p.Pro63His | missense_variant | 4/19 | ||
RAD54L | NM_001370766.1 | c.-353C>A | 5_prime_UTR_variant | 3/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD54L | ENST00000371975.9 | c.188C>A | p.Pro63His | missense_variant | 3/18 | 1 | NM_003579.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251482Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135918
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461884Hom.: 0 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727240
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Colon adenocarcinoma Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 03, 1999 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at