chr7-4801784-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018059.5(RADIL):c.2711C>T(p.Thr904Met) variant causes a missense change. The variant allele was found at a frequency of 0.000106 in 1,610,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00013 ( 0 hom., cov: 34)
Exomes 𝑓: 0.00010 ( 0 hom. )
Consequence
RADIL
NM_018059.5 missense
NM_018059.5 missense
Scores
6
5
8
Clinical Significance
Conservation
PhyloP100: 4.34
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]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.24439234).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RADIL | NM_018059.5 | c.2711C>T | p.Thr904Met | missense_variant | 12/15 | ENST00000399583.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RADIL | ENST00000399583.4 | c.2711C>T | p.Thr904Met | missense_variant | 12/15 | 5 | NM_018059.5 | P1 | |
RADIL | ENST00000472999.5 | n.735C>T | non_coding_transcript_exon_variant | 2/5 | 1 | ||||
RADIL | ENST00000473130.5 | n.1322C>T | non_coding_transcript_exon_variant | 8/11 | 2 | ||||
RADIL | ENST00000445392.5 | c.*1482C>T | 3_prime_UTR_variant, NMD_transcript_variant | 12/15 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152208Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.000186 AC: 43AN: 231276Hom.: 1 AF XY: 0.000203 AC XY: 26AN XY: 127778
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GnomAD4 exome AF: 0.000104 AC: 151AN: 1457898Hom.: 0 Cov.: 37 AF XY: 0.000131 AC XY: 95AN XY: 725090
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GnomAD4 genome AF: 0.000131 AC: 20AN: 152326Hom.: 0 Cov.: 34 AF XY: 0.000148 AC XY: 11AN XY: 74478
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2023 | The c.2711C>T (p.T904M) alteration is located in exon 12 (coding exon 11) of the RADIL gene. This alteration results from a C to T substitution at nucleotide position 2711, causing the threonine (T) at amino acid position 904 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MVP
MPC
ClinPred
D
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at