rs1048771
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Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_003579.4(RAD54L):c.2190C>A(p.Ala730=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,538 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )
Consequence
RAD54L
NM_003579.4 synonymous
NM_003579.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.21
Genes affected
RAD54L (HGNC:9826): (RAD54 like) The protein encoded by this gene belongs to the DEAD-like helicase superfamily, and shares similarity with Saccharomyces cerevisiae Rad54, a protein known to be involved in the homologous recombination and repair of DNA. This protein has been shown to play a role in homologous recombination related repair of DNA double-strand breaks. The binding of this protein to double-strand DNA induces a DNA topological change, which is thought to facilitate homologous DNA paring, and stimulate DNA recombination. Alternative splicing results in multiple transcript variants encoding the same protein.[provided by RefSeq, Dec 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.44).
BP7
Synonymous conserved (PhyloP=1.21 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| RAD54L | NM_003579.4 | c.2190C>A | p.Ala730= | synonymous_variant | 18/18 | ENST00000371975.9 | NP_003570.2 | |
| LRRC41 | NM_006369.5 | c.*637G>T | 3_prime_UTR_variant | 10/10 | ENST00000617190.5 | NP_006360.3 | ||
| RAD54L | NM_001142548.2 | c.2190C>A | p.Ala730= | synonymous_variant | 19/19 | NP_001136020.1 | ||
| RAD54L | NM_001370766.1 | c.1650C>A | p.Ala550= | synonymous_variant | 18/18 | NP_001357695.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| RAD54L | ENST00000371975.9 | c.2190C>A | p.Ala730= | synonymous_variant | 18/18 | 1 | NM_003579.4 | ENSP00000361043 | P1 | |
| LRRC41 | ENST00000617190.5 | c.*637G>T | 3_prime_UTR_variant | 10/10 | 1 | NM_006369.5 | ENSP00000477792 | P1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250040Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135206
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461538Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727040
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GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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