chr20-1244118-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001384355.1(RAD21L1):c.1256G>A(p.Gly419Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000591 in 1,549,678 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001384355.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD21L1 | NM_001384355.1 | c.1256G>A | p.Gly419Asp | missense_variant | 11/14 | ENST00000683101.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD21L1 | ENST00000683101.1 | c.1256G>A | p.Gly419Asp | missense_variant | 11/14 | NM_001384355.1 | A1 | ||
RAD21L1 | ENST00000409241.5 | c.1256G>A | p.Gly419Asp | missense_variant | 11/14 | 1 | P4 | ||
RAD21L1 | ENST00000402452.5 | c.1256G>A | p.Gly419Asp | missense_variant | 11/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000375 AC: 57AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000192 AC: 30AN: 156182Hom.: 0 AF XY: 0.000193 AC XY: 16AN XY: 82746
GnomAD4 exome AF: 0.000615 AC: 859AN: 1397368Hom.: 1 Cov.: 28 AF XY: 0.000617 AC XY: 425AN XY: 689328
GnomAD4 genome ? AF: 0.000374 AC: 57AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000349 AC XY: 26AN XY: 74482
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | 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