7-4799634-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_018059.5(RADIL):​c.3118C>A​(p.Leu1040Met) variant causes a missense change. The variant allele was found at a frequency of 0.000000688 in 1,452,834 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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: 6.9e-7 ( 0 hom. )

Consequence

RADIL
NM_018059.5 missense

Scores

1
18

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.85
Variant links:
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 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=0.13838795).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RADILNM_018059.5 linkc.3118C>A p.Leu1040Met missense_variant Exon 14 of 15 ENST00000399583.4 NP_060529.4 Q96JH8-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RADILENST00000399583.4 linkc.3118C>A p.Leu1040Met missense_variant Exon 14 of 15 5 NM_018059.5 ENSP00000382492.3 Q96JH8-4

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
AF:
6.88e-7
AC:
1
AN:
1452834
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
722060
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.02e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.098
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.59
CADD
Benign
21
DANN
Benign
0.85
DEOGEN2
Benign
0.012
T
Eigen
Benign
-0.30
Eigen_PC
Benign
-0.18
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Benign
0.59
T
M_CAP
Benign
0.027
D
MetaRNN
Benign
0.14
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
1.5
L
PrimateAI
Benign
0.36
T
PROVEAN
Benign
0.59
N
REVEL
Benign
0.052
Sift
Benign
0.29
T
Sift4G
Benign
0.27
T
Polyphen
0.0030
B
Vest4
0.25
MutPred
0.50
Gain of MoRF binding (P = 0.0665);
MVP
0.25
MPC
0.046
ClinPred
0.28
T
GERP RS
3.4
Varity_R
0.079
gMVP
0.34

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-4839265; API