1-46278228-C-T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_003579.4(RAD54L):c.2190C>T(p.Ala730Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 1,613,356 control chromosomes in the GnomAD database, including 17,922 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_003579.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD54L | NM_003579.4 | c.2190C>T | p.Ala730Ala | synonymous_variant | Exon 18 of 18 | ENST00000371975.9 | NP_003570.2 | |
LRRC41 | NM_006369.5 | c.*637G>A | 3_prime_UTR_variant | Exon 10 of 10 | ENST00000617190.5 | NP_006360.3 | ||
RAD54L | NM_001142548.2 | c.2190C>T | p.Ala730Ala | synonymous_variant | Exon 19 of 19 | NP_001136020.1 | ||
RAD54L | NM_001370766.1 | c.1650C>T | p.Ala550Ala | synonymous_variant | Exon 18 of 18 | NP_001357695.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD54L | ENST00000371975.9 | c.2190C>T | p.Ala730Ala | synonymous_variant | Exon 18 of 18 | 1 | NM_003579.4 | ENSP00000361043.4 | ||
LRRC41 | ENST00000617190 | c.*637G>A | 3_prime_UTR_variant | Exon 10 of 10 | 1 | NM_006369.5 | ENSP00000477792.1 |
Frequencies
GnomAD3 genomes AF: 0.108 AC: 16389AN: 151962Hom.: 1239 Cov.: 32
GnomAD3 exomes AF: 0.152 AC: 37888AN: 250040Hom.: 4144 AF XY: 0.166 AC XY: 22406AN XY: 135206
GnomAD4 exome AF: 0.132 AC: 193512AN: 1461276Hom.: 16682 Cov.: 32 AF XY: 0.140 AC XY: 101963AN XY: 726888
GnomAD4 genome AF: 0.108 AC: 16390AN: 152080Hom.: 1240 Cov.: 32 AF XY: 0.113 AC XY: 8387AN XY: 74368
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as 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. -
RAD54L-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
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Hereditary breast ovarian cancer syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at