chr20-1244070-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001384355.1(RAD21L1):c.1208A>G(p.Asn403Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000117 in 1,550,450 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).
Frequency
Consequence
NM_001384355.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RAD21L1 | NM_001384355.1 | c.1208A>G | p.Asn403Ser | missense_variant | 11/14 | ENST00000683101.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RAD21L1 | ENST00000683101.1 | c.1208A>G | p.Asn403Ser | missense_variant | 11/14 | NM_001384355.1 | A1 | ||
RAD21L1 | ENST00000409241.5 | c.1208A>G | p.Asn403Ser | missense_variant | 11/14 | 1 | P4 | ||
RAD21L1 | ENST00000402452.5 | c.1208A>G | p.Asn403Ser | missense_variant | 11/14 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000578 AC: 88AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 26AN: 155940Hom.: 0 AF XY: 0.000121 AC XY: 10AN XY: 82624
GnomAD4 exome AF: 0.0000665 AC: 93AN: 1398114Hom.: 0 Cov.: 28 AF XY: 0.0000537 AC XY: 37AN XY: 689558
GnomAD4 genome ? AF: 0.000578 AC: 88AN: 152336Hom.: 0 Cov.: 32 AF XY: 0.000591 AC XY: 44AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2021 | The c.1208A>G (p.N403S) alteration is located in exon 11 (coding exon 10) of the RAD21L1 gene. This alteration results from a A to G substitution at nucleotide position 1208, causing the asparagine (N) at amino acid position 403 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at