chr1-46261290-G-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6
The NM_003579.4(RAD54L):āc.796G>Cā(p.Val266Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000103 in 1,613,732 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V266M) has been classified as Uncertain significance.
Frequency
Consequence
NM_003579.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD54L | NM_003579.4 | c.796G>C | p.Val266Leu | missense_variant | 8/18 | ENST00000371975.9 | |
RAD54L | NM_001142548.2 | c.796G>C | p.Val266Leu | missense_variant | 9/19 | ||
RAD54L | NM_001370766.1 | c.256G>C | p.Val86Leu | missense_variant | 8/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD54L | ENST00000371975.9 | c.796G>C | p.Val266Leu | missense_variant | 8/18 | 1 | NM_003579.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000856 AC: 13AN: 151804Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251464Hom.: 0 AF XY: 0.0000441 AC XY: 6AN XY: 135904
GnomAD4 exome AF: 0.000105 AC: 153AN: 1461810Hom.: 0 Cov.: 36 AF XY: 0.000117 AC XY: 85AN XY: 727204
GnomAD4 genome AF: 0.0000856 AC: 13AN: 151922Hom.: 0 Cov.: 31 AF XY: 0.0000673 AC XY: 5AN XY: 74254
ClinVar
Submissions by phenotype
Non-Hodgkin lymphoma Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 23, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at