rs2306921
Positions:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018059.5(RADIL):c.3118C>T(p.Leu1040=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000344 in 1,452,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 34)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
RADIL
NM_018059.5 synonymous
NM_018059.5 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 3.85
Genes affected
RADIL (HGNC:22226): (Rap associating with DIL domain) Predicted to enable GTPase binding activity. Acts upstream of or within substrate adhesion-dependent cell spreading. Located in microtubule. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.59).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RADIL | NM_018059.5 | c.3118C>T | p.Leu1040= | synonymous_variant | 14/15 | ENST00000399583.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RADIL | ENST00000399583.4 | c.3118C>T | p.Leu1040= | synonymous_variant | 14/15 | 5 | NM_018059.5 | P1 | |
RADIL | ENST00000472999.5 | n.1142C>T | non_coding_transcript_exon_variant | 4/5 | 1 | ||||
RADIL | ENST00000473130.5 | n.1729C>T | non_coding_transcript_exon_variant | 10/11 | 2 | ||||
RADIL | ENST00000445392.5 | c.*1889C>T | 3_prime_UTR_variant, NMD_transcript_variant | 14/15 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 genomes
?
Cov.:
34
GnomAD4 exome AF: 0.00000344 AC: 5AN: 1452834Hom.: 0 Cov.: 33 AF XY: 0.00000277 AC XY: 2AN XY: 722060
GnomAD4 exome
AF:
AC:
5
AN:
1452834
Hom.:
Cov.:
33
AF XY:
AC XY:
2
AN XY:
722060
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Cov.: 34
GnomAD4 genome
?
Cov.:
34
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at