20-1239354-T-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001384355.1(RAD21L1):c.689T>A(p.Met230Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000774 in 1,550,172 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RAD21L1 | NM_001384355.1 | c.689T>A | p.Met230Lys | missense_variant | 7/14 | ENST00000683101.1 | NP_001371284.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAD21L1 | ENST00000683101.1 | c.689T>A | p.Met230Lys | missense_variant | 7/14 | NM_001384355.1 | ENSP00000507397 | A1 | ||
RAD21L1 | ENST00000409241.5 | c.689T>A | p.Met230Lys | missense_variant | 7/14 | 1 | ENSP00000386414 | P4 | ||
RAD21L1 | ENST00000402452.5 | c.689T>A | p.Met230Lys | missense_variant | 7/14 | 5 | ENSP00000385925 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000715 AC: 10AN: 1397982Hom.: 0 Cov.: 28 AF XY: 0.00000580 AC XY: 4AN XY: 689600
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 14, 2023 | The c.689T>A (p.M230K) alteration is located in exon 7 (coding exon 6) of the RAD21L1 gene. This alteration results from a T to A substitution at nucleotide position 689, causing the methionine (M) at amino acid position 230 to be replaced by a lysine (K). 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