8-116850723-G-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_006265.3(RAD21):c.1515C>G(p.Pro505Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000459 in 1,613,220 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_006265.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD21 | NM_006265.3 | c.1515C>G | p.Pro505Pro | synonymous_variant | Exon 12 of 14 | ENST00000297338.7 | NP_006256.1 | |
LOC112268030 | XR_002956724.2 | n.*135G>C | downstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00263 AC: 400AN: 151996Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000601 AC: 151AN: 251208Hom.: 1 AF XY: 0.000449 AC XY: 61AN XY: 135768
GnomAD4 exome AF: 0.000233 AC: 341AN: 1461106Hom.: 2 Cov.: 31 AF XY: 0.000168 AC XY: 122AN XY: 726898
GnomAD4 genome AF: 0.00263 AC: 400AN: 152114Hom.: 1 Cov.: 32 AF XY: 0.00254 AC XY: 189AN XY: 74356
ClinVar
Submissions by phenotype
not provided Benign:2
RAD21: BP4, BP7 -
- -
Inborn genetic diseases Benign:1
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. -
RAD21-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). -
Cornelia de Lange syndrome 4 Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at